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RGD DISEASE ONTOLOGY - ANNOTATIONS

RGD uses the Human Disease Ontology (DO, https://disease-ontology.org/) for disease curation across species. RGD automatically downloads each new release of the ontology on a monthly basis. Some additional terms which are required for RGD's curation purposes but are not currently covered in the official version of DO have been added. As corresponding terms are added to DO, these custom terms are retired and the DO terms substituted in existing annotations and subsequently used for curation.

Term:Avitaminosis
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Accession:DOID:9004644 term browser browse the term
Definition:A condition due to a deficiency of one or more essential vitamins. (Dorland, 27th ed)
Synonyms:exact_synonym: Avitaminoses;   Vitamin Deficiencies;   Vitamin Deficiency
 primary_id: MESH:D001361;   RDO:0004924
For additional species annotation, visit the Alliance of Genome Resources.


show annotations for term's descendants           Sort by:
 
autosomal dominant hypophosphatemic rickets term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Fgf23 fibroblast growth factor 23 ISO OMIM NCBI chrNW_004936606:4,555,034...4,561,961 JBrowse link
autosomal recessive hypophosphatemic rickets term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Dmp1 dentin matrix acidic phosphoprotein 1 ISO ClinVar Annotator: match by term: Hypophosphatemic Rickets, Recessive ClinVar NCBI chrNW_004936905:419,478...427,335 JBrowse link
G LOC101964456 ectonucleotide pyrophosphatase/phosphodiesterase family member 1 ISO ClinVar Annotator: match by term: Hypophosphatemic Rickets, Recessive ClinVar PMID:24033266, PMID:28492532 NCBI chrNW_004937067:194,375...246,607 JBrowse link
choline deficiency disease term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Dnmt1 DNA methyltransferase 1 ISO mRNA:increased expression:liver: RGD PMID:17724018 RGD:9588267 NCBI chrNW_004936659:520,181...565,496 JBrowse link
G Dnmt3l DNA methyltransferase 3 like ISO mRNA:increased expression:liver: RGD PMID:17724018 RGD:9588267 NCBI chrNW_004936500:143,078...160,318 JBrowse link
G Mbd2 methyl-CpG binding domain protein 2 ISO DNA:hypermethylation:liver: RGD PMID:17724018 RGD:9588267 NCBI chrNW_004936497:9,512,350...9,619,250 JBrowse link
congenital intrinsic factor deficiency term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Cblif cobalamin binding intrinsic factor ISO OMIM NCBI chrNW_004936581:2,919,793...2,933,743 JBrowse link
cystathioninuria term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Cth cystathionine gamma-lyase ISO OMIM NCBI chrNW_004936591:1,619,446...1,643,667 JBrowse link
Familial Hypophosphatemic Rickets term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Clcn5 chloride voltage-gated channel 5 ISO CTD Direct Evidence: marker/mechanism CTD NCBI chrNW_004936721:1,552,312...1,602,360 JBrowse link
G Phex phosphate regulating endopeptidase homolog X-linked ISO CTD Direct Evidence: marker/mechanism
ClinVar Annotator: match by term: Familial Hypophosphatemic Rickets
CTD
ClinVar
PMID:3414685, PMID:9097956, PMID:9199930, PMID:9430241, PMID:11414762, PMID:11468271, PMID:12727977, PMID:18625346, PMID:18775977, PMID:24684036, PMID:25741868, PMID:28492532, PMID:29858904 NCBI chrNW_004936624:2,124,479...2,312,847 JBrowse link
G Vdr vitamin D receptor ISO ClinVar Annotator: match by term: RICKETS, HEREDITARY VITAMIN D-RESISTANT ClinVar PMID:1652893, PMID:2174914, PMID:2177843, PMID:2557627, PMID:2558018, PMID:2849209, PMID:3024987, PMID:8392085, PMID:8675579, PMID:8862631, PMID:8961271, PMID:9005998, PMID:9360557, PMID:9495519, PMID:10707958, PMID:11564167, PMID:17130574, PMID:17371163, PMID:17970811, PMID:18159135, PMID:18279374, PMID:18593774, PMID:19682379, PMID:20200114, PMID:21168462, PMID:21931507, PMID:22992668, PMID:23180655, PMID:24033266, PMID:24073221, PMID:25741868, PMID:26177022, PMID:26198224, PMID:26590811, PMID:26631034, PMID:26911666, PMID:27164139, PMID:27607899, PMID:27778467, PMID:28492532 NCBI chrNW_004936512:5,741,836...5,800,999 JBrowse link
familial isolated deficiency of vitamin E term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Apoa1 apolipoprotein A1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:18458655 NCBI chrNW_004936542:2,111,055...2,112,626 JBrowse link
G Apob apolipoprotein B ISO CTD Direct Evidence: marker/mechanism CTD PMID:18458655 NCBI chrNW_004936493:10,509,118...10,549,144 JBrowse link
G Ttpa alpha tocopherol transfer protein ISO OMIM NCBI chrNW_004936496:10,409,948...10,466,722 JBrowse link
folic acid deficiency anemia term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Dhfr dihydrofolate reductase ISO CTD Direct Evidence: marker/mechanism CTD PMID:21310277 NCBI chrNW_004936469:67,962...83,116 JBrowse link
G Igf1 insulin like growth factor 1 ISO protein:decreased expression:serum, cranial bone (rat) RGD PMID:16111879 RGD:12910463 NCBI chrNW_004936492:11,709,623...11,784,028 JBrowse link
hereditary folate malabsorption term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Sarm1 sterile alpha and TIR motif containing 1 ISO ClinVar Annotator: match by term: Hereditary Folate Malabsorption
ClinVar Annotator: match by term: Congenital defect of folate absorption
ClinVar PMID:11807405, PMID:17129779, PMID:17446347, PMID:20686069 NCBI chrNW_004936538:4,526,713...4,546,861 JBrowse link
G Slc46a1 solute carrier family 46 member 1 ISO OMIM NCBI chrNW_004936538:4,549,032...4,642,870 JBrowse link
hereditary hypophosphatemic rickets with hypercalciuria term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Pth parathyroid hormone ISO protein:decreased expression:plasma (mouse) RGD PMID:19570882 RGD:7242924 NCBI chrNW_004936528:5,081,569...5,084,030 JBrowse link
G Slc34a1 solute carrier family 34 member 1 ISO DNA:deletions, snps:multiple (human) RGD PMID:16358215, PMID:19570882 RGD:7242924, RGD:7242925 NCBI chrNW_004936597:1,667,700...1,684,533 JBrowse link
G Slc34a3 solute carrier family 34 member 3 ISO OMIM NCBI chrNW_004936669:755,091...760,365 JBrowse link
homocystinuria term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Cbs cystathionine beta-synthase ISO OMIM NCBI chrNW_004936500:976,043...1,003,559 JBrowse link
G Mmachc metabolism of cobalamin associated C ISO ClinVar Annotator: match by term: Homocystinuria ClinVar PMID:11261516, PMID:16311595, PMID:16714133, PMID:17853453, PMID:18245139, PMID:19370762, PMID:19700356, PMID:25398587, PMID:25672861, PMID:25689098, PMID:25741868, PMID:26825575, PMID:26990548, PMID:28492532 NCBI chrNW_004936474:26,636,277...26,641,486 JBrowse link
G Mthfr methylenetetrahydrofolate reductase ISO DNA:missense mutations, nonsense mutations:cds:multiple (human) RGD PMID:10679944 RGD:1601421 NCBI chrNW_004936474:623,438...637,849 JBrowse link
G Mtr 5-methyltetrahydrofolate-homocysteine methyltransferase ISO ClinVar Annotator: match by term: Homocystinuria ClinVar PMID:8968736, PMID:9235907, PMID:12068375, PMID:25526710, PMID:25558065, PMID:25741868, PMID:25856670, PMID:28492532, PMID:28666289, PMID:32581362 NCBI chrNW_004936484:16,087,924...16,180,089 JBrowse link
G Mtrr 5-methyltetrahydrofolate-homocysteine methyltransferase reductase ISO CTD Direct Evidence: marker/mechanism
ClinVar Annotator: match by term: Homocystinuria without methylmalonic aciduria
DNA:polymorphisms,mutations: :
CTD
ClinVar
RGD
PMID:10484769, PMID:12555939, PMID:15714522, PMID:24033266 RGD:5508189 NCBI chrNW_004936643:379,790...410,034 JBrowse link
G Pkhd1 PKHD1 ciliary IPT domain containing fibrocystin/polyductin ISO ClinVar Annotator: match by term: Cystathionine beta-synthase deficiency ClinVar PMID:25741868 NCBI chrNW_004936476:8,730,766...9,160,102 JBrowse link
Homocystinuria, Pyridoxine-Responsive term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Cbs cystathionine beta-synthase ISO ClinVar Annotator: match by term: Homocystinuria, pyridoxine-responsive ClinVar PMID:1301198, PMID:2056790, PMID:6711564, PMID:7506602, PMID:7611293, PMID:7635485, PMID:7762555, PMID:8353501, PMID:8528202, PMID:8554066, PMID:8755636, PMID:8803779, PMID:8940271, PMID:8990018, PMID:9156316, PMID:9232191, PMID:9361025, PMID:9587029, PMID:9708897, PMID:9864922, PMID:10215408, PMID:10328723, PMID:10338090, PMID:10364517, PMID:10408774, PMID:10531322, PMID:10807759, PMID:11230183, PMID:11343305, PMID:11359213, PMID:11434706, PMID:12007221, PMID:12124992, PMID:12269827, PMID:12552044, PMID:12686134, PMID:14635102, PMID:14722619, PMID:14722927, PMID:14972327, PMID:15087459, PMID:15146473, PMID:15192637, PMID:15365998, PMID:16245937, PMID:16307898, PMID:16375773, PMID:16479318, PMID:16619244, PMID:17072863, PMID:17540596, PMID:18201569, PMID:18805305, PMID:19232736, PMID:19819175, PMID:20066033, PMID:20490928, PMID:20506325, PMID:20567906, PMID:21520339, PMID:22069143, PMID:22267502, PMID:22333527, PMID:22612060, PMID:22738154, PMID:23592311, PMID:23974653, PMID:24033266, PMID:24211323, PMID:25044645, PMID:25218699, PMID:25331909, PMID:25516723, PMID:25741868, PMID:26750749, PMID:28488385, PMID:28492532, PMID:28583326, PMID:29650765, PMID:30311386 NCBI chrNW_004936500:976,043...1,003,559 JBrowse link
Homocystinuria-Megaloblastic Anemia due to Defect in Cobalamin Metabolism, CblE Complementation Type term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Mtrr 5-methyltetrahydrofolate-homocysteine methyltransferase reductase ISO OMIM NCBI chrNW_004936643:379,790...410,034 JBrowse link
Hypercarotenemia and Vitamin A Deficiency, Autosomal Dominant term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Bco1 beta-carotene oxygenase 1 ISO OMIM NCBI chrNW_004936475:28,859,222...28,890,407 JBrowse link
hyperhomocysteinemia term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Agt angiotensinogen ISO CTD Direct Evidence: marker/mechanism CTD PMID:24386282 NCBI chrNW_004936484:19,713,299...19,721,144 JBrowse link
G Ahcy adenosylhomocysteinase ISO RGD PMID:12208805 RGD:1598896 NCBI chrNW_004936561:6,314,797...6,333,961 JBrowse link
G Apoe apolipoprotein E treatment ISO RGD PMID:22762542 RGD:6903856 NCBI chrNW_004936706:1,512,438...1,516,805 JBrowse link
G Atp1a1 ATPase Na+/K+ transporting subunit alpha 1 ISO protein:decreased expression:cerebral cortex RGD PMID:23467881 RGD:11576285 NCBI chrNW_004936627:1,555,151...1,584,370 JBrowse link
G Bche butyrylcholinesterase ISO Protein:increased expression:serum RGD PMID:16442260 RGD:1599454 NCBI chrNW_004936707:1,784,338...1,913,401 JBrowse link
G Cbs cystathionine beta-synthase ISO CTD Direct Evidence: marker/mechanism
ClinVar Annotator: match by term: Hyperhomocysteinemia
mRNA:decreased expression, protein:decreased expression
CTD
ClinVar
RGD
PMID:7762555, PMID:12686134, PMID:16205833, PMID:16479318, PMID:16636197, PMID:17292331, PMID:19028542, PMID:19204075, PMID:21517828, PMID:22267502, PMID:22977242, PMID:25741868, PMID:28492532 RGD:1600624 NCBI chrNW_004936500:976,043...1,003,559 JBrowse link
G Cth cystathionine gamma-lyase ISO ClinVar Annotator: match by term: Homocysteine, total plasma, elevated ClinVar PMID:15151507 NCBI chrNW_004936591:1,619,446...1,643,667 JBrowse link
G Des desmin ISO CTD Direct Evidence: marker/mechanism CTD PMID:20116427 NCBI chrNW_004936569:1,807,902...1,814,936 JBrowse link
G Ece1 endothelin converting enzyme 1 ISO RGD PMID:19371338 RGD:4892572 NCBI chrNW_004936474:7,034,134...7,083,005 JBrowse link
G Ednra endothelin receptor type A ISO RGD PMID:19371338 RGD:4892572 NCBI chrNW_004936535:1,950,117...2,005,786 JBrowse link
G F12 coagulation factor XII treatment ISO RGD PMID:16046705 RGD:1601105 NCBI chrNW_004936597:1,687,511...1,694,782 JBrowse link
G F2 coagulation factor II, thrombin treatment ISO RGD PMID:16046705 RGD:1601105 NCBI chrNW_004936562:2,371,725...2,388,617 JBrowse link
G F8 coagulation factor VIII ISO RGD PMID:16046705 RGD:1601105 NCBI chrNW_004936927:189,359...301,791 JBrowse link
G G6pd glucose-6-phosphate dehydrogenase ISO protein:decreased expression:lung RGD PMID:21717134 RGD:10449171 NCBI chrNW_004936809:1,269,900...1,285,853 JBrowse link
G Gpx1 glutathione peroxidase 1 treatment ISO RGD PMID:24563435 RGD:11035307 NCBI chrNW_004936529:997,943...999,123 JBrowse link
G Gria1 glutamate ionotropic receptor AMPA type subunit 1 treatment ISO RGD PMID:25457025 RGD:13792697 NCBI chrNW_004936515:8,937,391...9,236,438 JBrowse link
G Grin2a glutamate ionotropic receptor NMDA type subunit 2A treatment ISO RGD PMID:25457025 RGD:13792697 NCBI chrNW_004936530:8,286,101...8,612,183 JBrowse link
G Grin2b glutamate ionotropic receptor NMDA type subunit 2B treatment ISO RGD PMID:25457025 RGD:13792697 NCBI chrNW_004936587:3,406,055...3,806,956 JBrowse link
G Icam1 intercellular adhesion molecule 1 ISO protein:increased expression:descending aorta, endothelial cells (rat) RGD PMID:20871618 RGD:4144131 NCBI chrNW_004936659:616,570...627,172 JBrowse link
G Il1b interleukin 1 beta ISO protein:increased expression:renal glomerulus (mouse) RGD PMID:22647887 RGD:7175168 NCBI chrNW_004936783:1,251,678...1,256,807 JBrowse link
G LOC101961866 coagulation factor X treatment ISO RGD PMID:16046705 RGD:1601105 NCBI chrNW_004936472:475,851...502,341 JBrowse link
G LOC101964621 glycine N-methyltransferase ISO CTD Direct Evidence: marker/mechanism CTD PMID:16317120 NCBI chrNW_004936476:16,961,734...16,965,487 JBrowse link
G LOC101966570 sodium/potassium-transporting ATPase subunit alpha-2 ISO protein:decreased expression:cerebral cortex RGD PMID:23467881 RGD:11576285 NCBI chrNW_004936740:489,357...514,235 JBrowse link
G Mmp9 matrix metallopeptidase 9 treatment ISO RGD PMID:24739303 RGD:13204791 NCBI chrNW_004936514:7,038,240...7,045,873 JBrowse link
G Mthfr methylenetetrahydrofolate reductase treatment ISO CTD Direct Evidence: marker/mechanism|therapeutic
DNA:missense mutations, nonsense mutations:cds:multiple (human)
associated with Ovarian Neoplasms; DNA:SNP: :677C>T (human)
CTD
RGD
PMID:10459572, PMID:10679944, PMID:12471611, PMID:15226090, PMID:16317120, PMID:16397167, PMID:16411416, PMID:16575899, PMID:17387702, PMID:18234410, PMID:18551038, PMID:19204075, PMID:19646848 RGD:10449400, RGD:1601421 NCBI chrNW_004936474:623,438...637,849 JBrowse link
G Mtr 5-methyltetrahydrofolate-homocysteine methyltransferase ISO RGD PMID:12068375 RGD:1601425 NCBI chrNW_004936484:16,087,924...16,180,089 JBrowse link
G Mtrr 5-methyltetrahydrofolate-homocysteine methyltransferase reductase ISO CTD Direct Evidence: marker/mechanism CTD PMID:16575899, PMID:17369066 NCBI chrNW_004936643:379,790...410,034 JBrowse link
G Ngf nerve growth factor ISO RGD PMID:21044172 RGD:5144149 NCBI chrNW_004936627:635,784...641,290 JBrowse link
G Nppb natriuretic peptide B ISO mRNA, protein:increased expression:heart, plasma RGD PMID:17303690 RGD:1642265 NCBI chrNW_004936474:683,325...684,662 JBrowse link
G Pon1 paraoxonase 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:17292331, PMID:19028542 NCBI chrNW_004936585:4,954,871...4,979,560 JBrowse link
G Pycard PYD and CARD domain containing ISO CTD Direct Evidence: marker/mechanism CTD PMID:22647887 NCBI chrNW_004936501:13,550,702...13,552,774 JBrowse link
G Slc46a1 solute carrier family 46 member 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:19204075 NCBI chrNW_004936538:4,549,032...4,642,870 JBrowse link
G Sod2 superoxide dismutase 2 treatment ISO RGD PMID:24563435 RGD:11035307 NCBI chrNW_004936489:11,178,338...11,191,601 JBrowse link
G Timp1 TIMP metallopeptidase inhibitor 1 treatment ISO RGD PMID:24739303 RGD:13204791 NCBI chrNW_004936502:13,345,936...13,350,170 JBrowse link
G Tnf tumor necrosis factor ISO CTD Direct Evidence: marker/mechanism CTD PMID:12615666 NCBI chrNW_004936727:1,936,066...1,937,766 JBrowse link
Hypophosphatemic Rickets term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Dmp1 dentin matrix acidic phosphoprotein 1 ISO ClinVar Annotator: match by term: Hypophosphatemic rickets ClinVar PMID:24033266 NCBI chrNW_004936905:419,478...427,335 JBrowse link
G Fam20c FAM20C golgi associated secretory pathway kinase ISO RGD PMID:22615579 RGD:11558021 NCBI chrNW_004936754:596,878...649,585 JBrowse link
G Fgf23 fibroblast growth factor 23 ISO RGD PMID:14988389 RGD:10044208 NCBI chrNW_004936606:4,555,034...4,561,961 JBrowse link
G Phex phosphate regulating endopeptidase homolog X-linked ISO ClinVar Annotator: match by term: Hypophosphatemic rickets ClinVar PMID:25741868 NCBI chrNW_004936624:2,124,479...2,312,847 JBrowse link
G Vdr vitamin D receptor ISO ClinVar Annotator: match by term: HYPOCALCEMIC VITAMIN D-RESISTANT RICKETS ClinVar PMID:1652893, PMID:2174914, PMID:2177843, PMID:2557627, PMID:2558018, PMID:2849209, PMID:3024987, PMID:8392085, PMID:8675579, PMID:8862631, PMID:8961271, PMID:9005998, PMID:9360557, PMID:9495519, PMID:10707958, PMID:11564167, PMID:17130574, PMID:17371163, PMID:17970811, PMID:18159135, PMID:18279374, PMID:18593774, PMID:19682379, PMID:20200114, PMID:21168462, PMID:21931507, PMID:22992668, PMID:23180655, PMID:24033266, PMID:24073221, PMID:25741868, PMID:26177022, PMID:26198224, PMID:26590811, PMID:26631034, PMID:26911666, PMID:27164139, PMID:27607899, PMID:27778467, PMID:28492532 NCBI chrNW_004936512:5,741,836...5,800,999 JBrowse link
Hypophosphatemic Rickets, Autosomal Recessive, 1 term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Dmp1 dentin matrix acidic phosphoprotein 1 ISO OMIM NCBI chrNW_004936905:419,478...427,335 JBrowse link
Hypophosphatemic Rickets, Autosomal Recessive, 2 term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G LOC101964456 ectonucleotide pyrophosphatase/phosphodiesterase family member 1 ISO OMIM NCBI chrNW_004937067:194,375...246,607 JBrowse link
Imerslund-Grasbeck Syndrome term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Amn amnion associated transmembrane protein ISO ClinVar Annotator: match by term: Imerslund-Grasbeck syndrome ClinVar PMID:6741523, PMID:12590260, PMID:13852753, PMID:15024727, PMID:17114957, PMID:17285242, PMID:18181028, PMID:21750092, PMID:22078000, PMID:22631584, PMID:22929189, PMID:24156255, PMID:28492532 NCBI chrNW_004936835:961,840...970,287 JBrowse link
G Cubn cubilin ISO ClinVar Annotator: match by term: Imerslund-Grasbeck syndrome ClinVar PMID:10080186, PMID:10887099, PMID:15024727, PMID:15963748, PMID:22277662, PMID:22495309, PMID:22929189, PMID:24033266, PMID:24156255, PMID:25349199, PMID:25525159, PMID:25741868, PMID:27197912, PMID:28492532, PMID:31497480, PMID:31613795 NCBI chrNW_004936520:10,140,784...10,410,082 JBrowse link
G Traf3 TNF receptor associated factor 3 ISO ClinVar Annotator: match by term: Imerslund-Grasbeck syndrome ClinVar PMID:28492532 NCBI chrNW_004936835:844,747...955,900 JBrowse link
Imerslund-Grasbeck Syndrome 1 term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Amn amnion associated transmembrane protein ISO ClinVar Annotator: match by term: Enterocyte intrinsic factor receptor, defect of
ClinVar Annotator: match by term: Enterocyte cobalamin malabsorption
ClinVar Annotator: match by term: Megaloblastic anemia 1, Finnish type
ClinVar PMID:6741523, PMID:12590260, PMID:13852753, PMID:15024727, PMID:17114957, PMID:17285242, PMID:18181028, PMID:21750092, PMID:22078000, PMID:22631584, PMID:22929189, PMID:24156255, PMID:28492532 NCBI chrNW_004936835:961,840...970,287 JBrowse link
G Cblif cobalamin binding intrinsic factor ISO DNA:polymorphisms, missense mutations, splice sites:exon,intron:
protein:increased excretion:urine:
RGD PMID:10435666, PMID:15738392 RGD:11049583, RGD:11049586 NCBI chrNW_004936581:2,919,793...2,933,743 JBrowse link
G Cubn cubilin ISO OMIM NCBI chrNW_004936520:10,140,784...10,410,082 JBrowse link
G Traf3 TNF receptor associated factor 3 ISO ClinVar Annotator: match by term: Enterocyte intrinsic factor receptor, defect of ClinVar PMID:28492532 NCBI chrNW_004936835:844,747...955,900 JBrowse link
Imerslund-Grasbeck Syndrome 2 term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Amn amnion associated transmembrane protein ISO OMIM NCBI chrNW_004936835:961,840...970,287 JBrowse link
keratomalacia term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Rbp4 retinol binding protein 4 ISO CTD Direct Evidence: marker/mechanism CTD PMID:9888420 NCBI chrNW_004936601:1,401,215...1,410,195 JBrowse link
Methylenetetrahydrofolate Reductase Deficiency term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Mthfr methylenetetrahydrofolate reductase ISO OMIM NCBI chrNW_004936474:623,438...637,849 JBrowse link
methylmalonic aciduria and homocystinuria type cblC term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Dcdc2c doublecortin domain containing 2C ISO ClinVar Annotator: match by term: Methylmalonic acidemia with homocystinuria ClinVar PMID:25741868 NCBI chrNW_004936532:1,816,573...1,866,029 JBrowse link
G Hcfc1 host cell factor C1 ISO ClinVar Annotator: match by term: Methylmalonic acidemia with homocystinuria ClinVar PMID:24011988, PMID:25167861, PMID:25281006, PMID:25741868, PMID:26893841, PMID:27403441 NCBI chrNW_004936809:827,008...853,689 JBrowse link
G Mmachc metabolism of cobalamin associated C ISO OMIM NCBI chrNW_004936474:26,636,277...26,641,486 JBrowse link
G Prdx1 peroxiredoxin 1 ISO OMIM NCBI chrNW_004936474:26,641,776...26,653,291 JBrowse link
Methylmalonic Aciduria and Homocystinuria, cblJ Type term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Abcd4 ATP binding cassette subfamily D member 4 ISO OMIM NCBI chrNW_004936488:3,526,875...3,538,851 JBrowse link
Mthfr Deficiency, Thermolabile Type term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Mthfr methylenetetrahydrofolate reductase ISO ClinVar Annotator: match by term: MTHFR deficiency, thermolabile type ClinVar PMID:1522835, PMID:7564788, PMID:7647779, PMID:7741859, PMID:8542260, PMID:8554053, PMID:8554066, PMID:8616944, PMID:8771990, PMID:8826441, PMID:8837319, PMID:8892013, PMID:8903338, PMID:8981967, PMID:8994411, PMID:9133512, PMID:9192280, PMID:9244205, PMID:9341863, PMID:9372726, PMID:9453374, PMID:9545395, PMID:9545406, PMID:9737770, PMID:9789068, PMID:9798595, PMID:9843036, PMID:9863598, PMID:10196703, PMID:10323741, PMID:10440833, PMID:10677336, PMID:10732818, PMID:10869114, PMID:10930360, PMID:10958762, PMID:11121176, PMID:11140843, PMID:11418485, PMID:11590551, PMID:11742092, PMID:11752418, PMID:11781870, PMID:11807890, PMID:11863127, PMID:11888585, PMID:11929966, PMID:11938441, PMID:12080391, PMID:12095808, PMID:12154064, PMID:12165282, PMID:12196644, PMID:12221667, PMID:12356947, PMID:12383688, PMID:12384649, PMID:12387655, PMID:12400059, PMID:12406076, PMID:12428084, PMID:12453860, PMID:12529699, PMID:12560871, PMID:12796225, PMID:12915598, PMID:14647408, PMID:15051775, PMID:15054400, PMID:15103709, PMID:15154859, PMID:15173232, PMID:15534175, PMID:15543147, PMID:15565101, PMID:15704130, PMID:15729744, PMID:15781665, PMID:15806605, PMID:15808177, PMID:15951337, PMID:16013960, PMID:16019535, PMID:16172608, PMID:16244782, PMID:16365871, PMID:16402130, PMID:16432849, PMID:16462575, PMID:16463153, PMID:16470725, PMID:16501586, PMID:16712703, PMID:16800002, PMID:16870553, PMID:17180579, PMID:17284634, PMID:17323057, PMID:17350979, PMID:17436239, PMID:17488658, PMID:17512587, PMID:17543893, PMID:17726486, PMID:17898028, PMID:18458567, PMID:18583979, PMID:18704422, PMID:18987660, PMID:19159907, PMID:19307503, PMID:19648163, PMID:20154341, PMID:20638924, PMID:21605004, PMID:21644011, PMID:21747412, PMID:22143415, PMID:22838948, PMID:22992668, PMID:23089671, PMID:23488607, PMID:23648444, PMID:23775025, PMID:24241962, PMID:24637499, PMID:25007187, PMID:25065700, PMID:25110820, PMID:25227144, PMID:25303299, PMID:25778468, PMID:26014925, PMID:27399166, PMID:28696419, PMID:29683944, PMID:30311386 NCBI chrNW_004936474:623,438...637,849 JBrowse link
osteomalacia term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Fbn1 fibrillin 1 ISO protein:increased expression:cortical bone, trabecular bone (mouse) RGD PMID:11159866 RGD:7794797 NCBI chrNW_004936471:10,747,030...10,969,223 JBrowse link
G Mepe matrix extracellular phosphoglycoprotein ISO CTD Direct Evidence: marker/mechanism CTD PMID:11414762 NCBI chrNW_004936905:284,849...297,297 JBrowse link
pernicious anemia term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Cblif cobalamin binding intrinsic factor ISO RGD PMID:167441, PMID:4434116 RGD:11049584, RGD:11049587 NCBI chrNW_004936581:2,919,793...2,933,743 JBrowse link
pyridoxine deficiency anemia term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ahcy adenosylhomocysteinase ISO RGD PMID:11575573 RGD:1598897 NCBI chrNW_004936561:6,314,797...6,333,961 JBrowse link
renal osteodystrophy term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Pth parathyroid hormone ISO associated with Kidney Failure, Chronic; protein:decreased expression:serum (human) RGD PMID:18480316 RGD:7242687 NCBI chrNW_004936528:5,081,569...5,084,030 JBrowse link
rickets term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Casr calcium sensing receptor ISO RGD PMID:12671052 RGD:734698 NCBI chrNW_004936536:8,574,064...8,599,446 JBrowse link
G Clcn5 chloride voltage-gated channel 5 ISO ClinVar Annotator: match by term: Rickets ClinVar PMID:30311386 NCBI chrNW_004936721:1,552,312...1,602,360 JBrowse link
G Dmp1 dentin matrix acidic phosphoprotein 1 ISO ClinVar Annotator: match by term: Rickets ClinVar PMID:28492532, PMID:30311386 NCBI chrNW_004936905:419,478...427,335 JBrowse link
G LOC101972957 vitamin D 25-hydroxylase ISO ClinVar Annotator: match by term: Rickets ClinVar PMID:30311386 NCBI chrNW_004936528:3,881,630...3,897,613 JBrowse link
G LOC101978323 25-hydroxyvitamin D-1 alpha hydroxylase, mitochondrial ISO ClinVar Annotator: match by term: Vitamin D-Dependent Rickets
CTD Direct Evidence: marker/mechanism
vitamin D-dependent rickets type I, OMIM:264700;DNA:missense mutations: :R107H, G125E, R335P, P382S
RGD
ClinVar
CTD
PMID:9486994, PMID:11416220, PMID:16494812 RGD:1600874, RGD:734871 NCBI chrNW_004936646:1,899,686...1,904,104 JBrowse link
G Pth parathyroid hormone ISO CTD Direct Evidence: marker/mechanism CTD PMID:10375030 NCBI chrNW_004936528:5,081,569...5,084,030 JBrowse link
G Pth1r parathyroid hormone 1 receptor ISO CTD Direct Evidence: marker/mechanism CTD PMID:10375030 NCBI chrNW_004936596:674,088...693,191 JBrowse link
G Vdr vitamin D receptor ISO CTD Direct Evidence: marker/mechanism
ClinVar Annotator: match by term: Vitamin D-Dependent Rickets
VDDR II,OMIM:277440;DNA:point mutation:exon:p.G33D, p.R70G (human)
CTD
ClinVar
RGD
PMID:1338926, PMID:2849209, PMID:17451081, PMID:22466564, PMID:28492532 RGD:1624354 NCBI chrNW_004936512:5,741,836...5,800,999 JBrowse link
Subacute Combined Degeneration term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Cd40 CD40 molecule treatment ISO RGD PMID:16716410 RGD:2313422 NCBI chrNW_004936514:6,936,915...6,947,246 JBrowse link
G Cd40lg CD40 ligand treatment ISO protein:increased expression:cerebrospinal fluid RGD PMID:16716410 RGD:2313422 NCBI chrNW_004936513:10,607,617...10,620,403 JBrowse link
thiamine-responsive megaloblastic anemia syndrome term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Slc19a2 solute carrier family 19 member 2 ISO OMIM NCBI chrNW_004936481:17,197,133...17,225,435 JBrowse link
transcobalamin II deficiency term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Tcn2 transcobalamin 2 ISO OMIM NCBI chrNW_004936904:97,535...113,886 JBrowse link
Vitamin A Deficiency term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Bmp4 bone morphogenetic protein 4 ISO CTD Direct Evidence: marker/mechanism CTD PMID:16120438 NCBI chrNW_004936697:1,054,237...1,061,468 JBrowse link
G Dgat1 diacylglycerol O-acyltransferase 1 ISO mRNA:increased expression:aorta RGD PMID:17047345 RGD:13782261 NCBI chrNW_004936470:7,916,438...7,926,089 JBrowse link
G Hamp hepcidin antimicrobial peptide ISO mRNA:increased expression:liver RGD PMID:19217259 RGD:11041734 NCBI chrNW_004936570:1,009,344...1,010,654 JBrowse link
G Ireb2 iron responsive element binding protein 2 ISO mRNA:increased expression:liver (rat) RGD PMID:22154532 RGD:12904026 NCBI chrNW_004936471:36,547,552...36,601,327 JBrowse link
G LOC101977861 cytochrome P450 26A1 treatment ISO RGD PMID:22554462, PMID:25451926 RGD:13782197, RGD:13782256 NCBI chrNW_004936601:1,810,572...1,815,927 JBrowse link
G Lrat lecithin retinol acyltransferase ISO CTD Direct Evidence: marker/mechanism CTD PMID:16174770 NCBI chrNW_004936576:1,491,480...1,498,568 JBrowse link
G Parp1 poly(ADP-ribose) polymerase 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:18676402 NCBI chrNW_004936526:3,102,468...3,147,601 JBrowse link
G Rbp4 retinol binding protein 4 ISO CTD Direct Evidence: marker/mechanism CTD PMID:16157297 NCBI chrNW_004936601:1,401,215...1,410,195 JBrowse link
G Tgm1 transglutaminase 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:16146918 NCBI chrNW_004936722:292,999...306,540 JBrowse link
G Vcam1 vascular cell adhesion molecule 1 ISO protein:increased expression:aorta RGD PMID:21512820 RGD:7207803 NCBI chrNW_004936748:785,491...802,791 JBrowse link
Vitamin B Deficiency term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Agxt alanine--glyoxylate and serine--pyruvate aminotransferase ISO RGD PMID:12544342 RGD:1599455 NCBI chrNW_004936745:856,915...867,477 JBrowse link
vitamin B12 deficiency term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Abcd4 ATP binding cassette subfamily D member 4 ISO CTD Direct Evidence: marker/mechanism CTD PMID:22922874 NCBI chrNW_004936488:3,526,875...3,538,851 JBrowse link
G Amn amnion associated transmembrane protein ISO ClinVar Annotator: match by term: Cobalamin deficiency ClinVar PMID:25741868 NCBI chrNW_004936835:961,840...970,287 JBrowse link
G Calr calreticulin ISO protein:increased expression:kidney (rat) RGD PMID:25982389 RGD:11352764 NCBI chrNW_004936659:1,994,695...1,999,070 JBrowse link
G Cd40lg CD40 ligand treatment ISO RGD PMID:16716410 RGD:2313422 NCBI chrNW_004936513:10,607,617...10,620,403 JBrowse link
G Cfl1 cofilin 1 ISO protein:increased expression:kidney (rat) RGD PMID:25982389 RGD:11352764 NCBI chrNW_004936599:3,678,724...3,682,314 JBrowse link
G Mtr 5-methyltetrahydrofolate-homocysteine methyltransferase ISO protein:decreased expression,decreased activity:liver: RGD PMID:14646334 RGD:8694080 NCBI chrNW_004936484:16,087,924...16,180,089 JBrowse link
G Pon1 paraoxonase 1 ISO protein:decreased activity:serum (human) RGD PMID:22568797 RGD:11553830 NCBI chrNW_004936585:4,954,871...4,979,560 JBrowse link
Vitamin D Deficiency term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Bglap bone gamma-carboxyglutamate protein ISO RGD PMID:3105848 RGD:6483561 NCBI chrNW_004936580:5,480,023...5,482,288 JBrowse link
G LOC101978323 25-hydroxyvitamin D-1 alpha hydroxylase, mitochondrial susceptibility ISO associated with Diabetes, Gestational;DNA:polymorphism:promoter:g.-1260C>A RGD PMID:18476984 RGD:2307310 NCBI chrNW_004936646:1,899,686...1,904,104 JBrowse link
G Lrp2 LDL receptor related protein 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:10052453 NCBI chrNW_004936469:10,245,001...10,438,933 JBrowse link
G Nadsyn1 NAD synthetase 1 susceptibility ISO DNA:SNP: :rs10898191(human) RGD PMID:22785457 RGD:11251488 NCBI chrNW_004936794:1,394,975...1,423,807 JBrowse link
G Retn resistin ISO mRNA:increased expression:liver RGD PMID:21994008 RGD:7207230 NCBI chrNW_004936588:4,705,295...4,706,653 JBrowse link
G Vcam1 vascular cell adhesion molecule 1 ISO associated with obesity;protein:increased expression:serum: RGD PMID:22677566 RGD:7241033 NCBI chrNW_004936748:785,491...802,791 JBrowse link
G Vdr vitamin D receptor susceptibility ISO associated with nonalcoholic fatty liver disease; DNA:SNP: :rs2228570(human)
CTD Direct Evidence: marker/mechanism
RGD
CTD
PMID:9525346, PMID:30683615 RGD:14401752 NCBI chrNW_004936512:5,741,836...5,800,999 JBrowse link
Vitamin D Hydroxylation-Deficient Rickets, Type 1A term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G LOC101972957 vitamin D 25-hydroxylase ISO ClinVar Annotator: match by term: VITAMIN D DEPENDENCY, TYPE 1 ClinVar PMID:8201479, PMID:10969262, PMID:15128933, PMID:16549493, PMID:24033266, PMID:25942481, PMID:28548312 NCBI chrNW_004936528:3,881,630...3,897,613 JBrowse link
G LOC101978323 25-hydroxyvitamin D-1 alpha hydroxylase, mitochondrial ISO OMIM NCBI chrNW_004936646:1,899,686...1,904,104 JBrowse link
Vitamin D Hydroxylation-Deficient Rickets, Type 1B term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G LOC101972957 vitamin D 25-hydroxylase ISO OMIM NCBI chrNW_004936528:3,881,630...3,897,613 JBrowse link
Vitamin D-Dependent Rickets term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G LOC101978323 25-hydroxyvitamin D-1 alpha hydroxylase, mitochondrial ISO ClinVar Annotator: match by term: Vitamin D-Dependent Rickets ClinVar NCBI chrNW_004936646:1,899,686...1,904,104 JBrowse link
G Vdr vitamin D receptor ISO ClinVar Annotator: match by term: Vitamin D-Dependent Rickets ClinVar PMID:28492532 NCBI chrNW_004936512:5,741,836...5,800,999 JBrowse link
Vitamin D-Dependent Rickets, Type 2A term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Vdr vitamin D receptor treatment ISO OMIM
RGD
PMID:24693968 RGD:13432060 NCBI chrNW_004936512:5,741,836...5,800,999 JBrowse link
Vitamin E Deficiency term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Slc4a1 solute carrier family 4 member 1 (Diego blood group) ISO protein:increased degradation:erythrocyte, membrane (rat) RGD PMID:3458208 RGD:10450477 NCBI chrNW_004936541:718,577...727,420 JBrowse link
G Ttpa alpha tocopherol transfer protein ISO CTD Direct Evidence: marker/mechanism CTD PMID:11095717 NCBI chrNW_004936496:10,409,948...10,466,722 JBrowse link
vitamin K deficiency bleeding term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Bglap bone gamma-carboxyglutamate protein ISO RGD PMID:16869104 RGD:6483568 NCBI chrNW_004936580:5,480,023...5,482,288 JBrowse link
G Ggcx gamma-glutamyl carboxylase no_association ISO RGD PMID:11154138 RGD:11040513 NCBI chrNW_004936712:1,696,264...1,709,087 JBrowse link
Wernicke encephalopathy term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ptgs2 prostaglandin-endoperoxide synthase 2 ISO mRNA, protein:increased expression:medial thalamic group, inferior colliculus, neuron RGD PMID:18481165 RGD:2300278 NCBI chrNW_004936481:3,821,564...3,828,086 JBrowse link
G Tkt transketolase ISO CTD Direct Evidence: marker/mechanism CTD PMID:3762968 NCBI chrNW_004936473:3,950,846...3,978,778 JBrowse link
X-linked dominant hypophosphatemic rickets term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Bglap bone gamma-carboxyglutamate protein ISO mRNA:increased expression:long bone RGD PMID:22573557 RGD:7207229 NCBI chrNW_004936580:5,480,023...5,482,288 JBrowse link
G Fam20c FAM20C golgi associated secretory pathway kinase ISO mRNA:increased expression:long bone, osteoblast, osteocyte (mouse) RGD PMID:24710520 RGD:11560488 NCBI chrNW_004936754:596,878...649,585 JBrowse link
G Phex phosphate regulating endopeptidase homolog X-linked ISO OMIM NCBI chrNW_004936624:2,124,479...2,312,847 JBrowse link
X-linked recessive hypophosphatemic rickets term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Clcn5 chloride voltage-gated channel 5 ISO OMIM NCBI chrNW_004936721:1,552,312...1,602,360 JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  disease 11962
    Nutritional and Metabolic Diseases 3467
      nutrition disease 681
        Malnutrition 181
          nutritional deficiency disease 173
            Avitaminosis 96
              Ascorbic Acid Deficiency + 0
              Vitamin A Deficiency + 11
              Vitamin B Deficiency + 60
              Vitamin D Deficiency + 21
              Vitamin E Deficiency + 4
              vitamin K deficiency bleeding 2
Path 2
Term Annotations click to browse term
  disease 11962
    Nutritional and Metabolic Diseases 3467
      disease of metabolism 3467
        acquired metabolic disease 1992
          nutrition disease 681
            Malnutrition 181
              nutritional deficiency disease 173
                Avitaminosis 96
                  Ascorbic Acid Deficiency + 0
                  Vitamin A Deficiency + 11
                  Vitamin B Deficiency + 60
                  Vitamin D Deficiency + 21
                  Vitamin E Deficiency + 4
                  vitamin K deficiency bleeding 2
paths to the root

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RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.