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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:skin benign neoplasm
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Accession:DOID:3165 term browser browse the term
Definition:A benign proliferation in the skin.
Synonyms:exact_synonym: benign neoplasm of skin;   benign tumor of skin;   neoplasm of skin;   neoplasm of skin by site;   skin neoplasm;   tumor of the skin
 primary_id: RDO:9000113
 xref: NCI:C3372
For additional species annotation, visit the Alliance of Genome Resources.


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skin benign neoplasm term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Hras HRas proto-oncogene, GTPase ISO associated with Nevus, Sebaceous of Jadassohn;DNA:mutation:cds:c.37G>C(p.G13R)(human) RGD PMID:22683711 RGD:11098548 NCBI chrNW_004936888:375,372...378,125 JBrowse link
G Ptch1 patched 1 ISO ClinVar Annotator: match by term: Tumor of the skin ClinVar PMID:30311386 NCBI chrNW_004936626:4,241,993...4,301,919 JBrowse link
angiokeratoma term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Gla galactosidase alpha ISO CTD Direct Evidence: therapeutic CTD PMID:19925601 NCBI chrNW_004936813:474,938...484,753 JBrowse link
G Naga alpha-N-acetylgalactosaminidase ISO Kanzaki Disease, OMIM:609242, DNA:point mutation:exon:R329W RGD PMID:8040340 RGD:1600558 NCBI chrNW_004936718:31,946...55,822 JBrowse link
anogenital venereal wart term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ccl20 C-C motif chemokine ligand 20 ISO protein:decreased expression:skin RGD PMID:17545018 RGD:7483603 NCBI chrNW_004936525:8,238,128...8,240,974 JBrowse link
G Il12b interleukin 12B treatment ISO RGD PMID:16114559 RGD:7829774 NCBI chrNW_004936515:4,056,214...4,066,121 JBrowse link
G Il4 interleukin 4 treatment ISO RGD PMID:16114559 RGD:7829774 NCBI chrNW_004936647:2,510,457...2,518,576 JBrowse link
G Ptpn11 protein tyrosine phosphatase non-receptor type 11 ISO protein:increased expression:foreskin RGD PMID:18543080 RGD:39128248 NCBI chrNW_004936668:2,602,261...2,687,903 JBrowse link
G Ptpn6 protein tyrosine phosphatase non-receptor type 6 ISO protein:increased expression:foreskin RGD PMID:18543080 RGD:39128248 NCBI chrNW_004936709:864,206...884,630 JBrowse link
G Serpinf1 serpin family F member 1 disease_progression ISO mRNA, protein:decreased expression:skin of body (human) RGD PMID:23569025 RGD:27226706 NCBI chrNW_004936538:7,885,816...7,898,308 JBrowse link
capillary hemangioma term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Col1a1 collagen type I alpha 1 chain ISO ClinVar Annotator: match by term: Capillary hemangioma ClinVar PMID:25741868, PMID:30311386 NCBI chrNW_004936490:11,448,552...11,465,836 JBrowse link
G Npc1 NPC intracellular cholesterol transporter 1 ISO ClinVar Annotator: match by term: Capillary hemangiomas ClinVar PMID:25741868 NCBI chrNW_004936550:2,983,172...3,032,222 JBrowse link
Capillary Hemangioma, Infantile term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Antxr1 ANTXR cell adhesion molecule 1 ISO OMIM NCBI chrNW_004936491:13,288,986...13,516,878 JBrowse link
G Flt4 fms related receptor tyrosine kinase 4 ISO OMIM NCBI chrNW_004936739:240,572...281,925 JBrowse link
G Kdr kinase insert domain receptor ISO OMIM NCBI chrNW_004936482:17,537,697...17,581,320 JBrowse link
G Myh9 myosin heavy chain 9 ISO ClinVar Annotator: match by term: Hemangioma, capillary infantile ClinVar NCBI chrNW_004936492:4,384,215...4,466,229 JBrowse link
G Slc2a1 solute carrier family 2 member 1 ISO RGD PMID:17554865 RGD:12879502 NCBI chrNW_004936474:24,205,878...24,236,611 JBrowse link
cerebellar angioblastoma term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Vhl von Hippel-Lindau tumor suppressor ISO ClinVar Annotator: match by term: Cerebellar hemangioblastoma ClinVar PMID:25741868, PMID:28492532 NCBI chrNW_004936602:3,135,790...3,140,622 JBrowse link
epidermodysplasia verruciformis term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Tmc6 transmembrane channel like 6 ISO CTD Direct Evidence: marker/mechanism
ClinVar Annotator: match by term: Epidermodysplasia verruciformis
CTD
ClinVar
PMID:15042430, PMID:17139267, PMID:25741868, PMID:28492532 NCBI chrNW_004936594:2,743,466...2,759,482 JBrowse link
G Tmc8 transmembrane channel like 8 ISO ClinVar Annotator: match by term: Epidermodysplasia verruciformis ClinVar PMID:12426567, PMID:22158547, PMID:25741868, PMID:28492532 NCBI chrNW_004936594:2,760,649...2,768,438 JBrowse link
Epidermodysplasia Verruciformis 1 term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Tmc6 transmembrane channel like 6 ISO OMIM NCBI chrNW_004936594:2,743,466...2,759,482 JBrowse link
G Tmc8 transmembrane channel like 8 ISO ClinVar Annotator: match by term: EPIDERMODYSPLASIA VERRUCIFORMIS, SUSCEPTIBILITY TO, 1 ClinVar PMID:25741868, PMID:28492532 NCBI chrNW_004936594:2,760,649...2,768,438 JBrowse link
Epidermodysplasia Verruciformis 2 term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Tmc8 transmembrane channel like 8 ISO OMIM NCBI chrNW_004936594:2,760,649...2,768,438 JBrowse link
Epidermodysplasia Verruciformis 3 term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Cib1 calcium and integrin binding 1 ISO OMIM NCBI chrNW_004936483:15,963,863...15,967,458 JBrowse link
Epidermodysplasia Verruciformis 4 term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Rhoh ras homolog family member H susceptibility ISO ClinVar Annotator: match by term: EPIDERMODYSPLASIA VERRUCIFORMIS, SUSCEPTIBILITY TO, 4 OMIM
ClinVar
PMID:22850876 NCBI chrNW_004936482:7,721,815...7,723,395 JBrowse link
Epidermodysplasia Verruciformis 5 term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Il7 interleukin 7 susceptibility ISO ClinVar Annotator: match by term: EPIDERMODYSPLASIA VERRUCIFORMIS, SUSCEPTIBILITY TO, 5 OMIM
ClinVar
PMID:25981006 NCBI chrNW_004936702:110,625...162,957 JBrowse link
hemangioblastoma term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Hif1a hypoxia inducible factor 1 subunit alpha ISO CTD Direct Evidence: marker/mechanism CTD PMID:15341671 NCBI chrNW_004936495:5,770,988...5,816,157 JBrowse link
G Ndrg1 N-myc downstream regulated 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:15341671 NCBI chrNW_004936470:16,051,291...16,102,563 JBrowse link
leiomyoma cutis term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Fh fumarate hydratase ISO ClinVar Annotator: match by term: Multiple cutaneous leiomyomas ClinVar PMID:11865300, PMID:12761039, PMID:16575891, PMID:21929734, PMID:22069215, PMID:22595425, PMID:22703879, PMID:24728327, PMID:25741868, PMID:27037871, PMID:28492532, PMID:29909963, PMID:30967997 NCBI chrNW_004936526:8,936,096...8,965,155 JBrowse link
Malignant Granular Cell Tumor term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Brd7 bromodomain containing 7 ISO ClinVar Annotator: match by term: malignant granular cell tumor ClinVar NCBI chrNW_004936475:3,394,423...3,432,998 JBrowse link
Muir-Torre syndrome term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Mlh1 mutL homolog 1 ISO OMIM NCBI chrNW_004936473:26,556,636...26,600,830 JBrowse link
G Msh2 mutS homolog 2 ISO OMIM NCBI chrNW_004936508:4,943,987...5,013,356 JBrowse link
Nasopalpebral Lipoma Coloboma Syndrome term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Zdbf2 zinc finger DBF-type containing 2 ISO ClinVar Annotator: match by term: Nasopalpebral lipoma coloboma syndrome ClinVar PMID:23636874, PMID:27139419 NCBI chrNW_004936631:2,649,792...2,686,430 JBrowse link
pilomatrixoma term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ctnnb1 catenin beta 1 ISO OMIM NCBI chrNW_004936473:29,999,542...30,034,610 JBrowse link
G Mutyh mutY DNA glycosylase ISO ClinVar Annotator: match by term: MUTYH-associated polyposis
ClinVar Annotator: match by term: EPITHELIOMA CALCIFICANS OF MALHERBE
ClinVar PMID:2084865, PMID:3561487, PMID:11818965, PMID:12393807, PMID:12606733, PMID:12853198, PMID:15188161, PMID:15236166, PMID:15366000, PMID:15635083, PMID:15890374, PMID:15931596, PMID:15987719, PMID:16134147, PMID:16140997, PMID:16207212, PMID:16287072, PMID:16338133, PMID:16455870, PMID:16492921, PMID:16557584, PMID:16616356, PMID:16890597, PMID:16941501, PMID:17081686, PMID:17122612, PMID:17161978, PMID:17219385, PMID:17273161, PMID:17368238, PMID:17369389, PMID:17489848, PMID:17581577, PMID:17674103, PMID:17703316, PMID:17874208, PMID:17931073, PMID:17949294, PMID:17956577, PMID:18091433, PMID:18301448, PMID:18414213, PMID:18422726, PMID:18495334, PMID:18506705, PMID:18515411, PMID:18534194, PMID:18564191, PMID:18787472, PMID:18992148, PMID:19032956, PMID:19245865, PMID:19279422, PMID:19394335, PMID:19506731, PMID:19527492, PMID:19531215, PMID:19725997, PMID:19732775, PMID:19793053, PMID:19806110, PMID:19836313, PMID:19953527, PMID:19998059, PMID:20063264, PMID:20418187, PMID:20618354, PMID:20663686, PMID:20725929, PMID:20848659, PMID:21063410, PMID:21171015, PMID:21178863, PMID:21443744, PMID:21520333, PMID:21815886, PMID:21952991, PMID:22158503, PMID:22266422, PMID:22297469, PMID:22473953, PMID:22538434, PMID:22703879, PMID:22744763, PMID:22773231, PMID:22865608, PMID:22926731, PMID:22976915, PMID:23035301, PMID:23108399, PMID:23322991, PMID:23361220, PMID:23507534, PMID:23561487, PMID:23605219, PMID:23625202, PMID:23729658, PMID:23805267, PMID:24033266, PMID:24082139, PMID:24278394, PMID:24444654, PMID:24470512, PMID:24569162, PMID:24691292, PMID:24728327, PMID:24763289, PMID:24799981, PMID:24953332, PMID:25368107, PMID:25525159, PMID:25590978, PMID:25637381, PMID:25741868, PMID:25820570, PMID:25892863, PMID:25980754, PMID:26446593, PMID:26467025, PMID:26556299, PMID:26673696, PMID:26681312, PMID:26689913, PMID:26694661, PMID:26822237, PMID:26845104, PMID:26902849, PMID:27145315, PMID:27194394, PMID:27705013, PMID:27829682, PMID:27870730, PMID:28135145, PMID:28141798, PMID:28152038, PMID:28251689, PMID:28492532, PMID:28533537, PMID:28634180, PMID:29330641, PMID:29406563, PMID:29478780, PMID:30311386, PMID:30487145 NCBI chrNW_004936474:26,484,316...26,492,652 JBrowse link
G Ovol1 ovo like transcriptional repressor 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:26873447 NCBI chrNW_004936599:3,732,335...3,742,749 JBrowse link
G Ovol2 ovo like zinc finger 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:26873447 NCBI chrNW_004936485:2,096,495...2,128,002 JBrowse link
Pulmonary Venoocclusive Disease 2 term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Eif2ak4 eukaryotic translation initiation factor 2 alpha kinase 4 ISO OMIM NCBI chrNW_004936471:3,423,792...3,527,089 JBrowse link
Schopf-Schulz-Passarge syndrome term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Wnt10a Wnt family member 10A ISO OMIM NCBI chrNW_004936569:1,309,140...1,321,923 JBrowse link
sebaceous gland neoplasm term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Cdkn1a cyclin dependent kinase inhibitor 1A ISO RGD PMID:12354803 RGD:8662839 NCBI chrNW_004936476:22,717,308...22,725,127 JBrowse link
G Lef1 lymphoid enhancer binding factor 1 ISO CTD Direct Evidence: marker/mechanism CTD PMID:16565724 NCBI chrNW_004936818:453,635...569,194 JBrowse link
seborrheic keratosis term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Anxa1 annexin A1 ISO RGD PMID:8919037 RGD:7421562 NCBI chrNW_004936503:9,124,314...9,142,372 JBrowse link
G Fgfr3 fibroblast growth factor receptor 3 ISO ClinVar Annotator: match by term: Keratosis Seborrheica ClinVar PMID:1908846, PMID:7773297, PMID:8589699, PMID:8858131, PMID:9677066, PMID:10073901, PMID:10471491, PMID:10696568, PMID:11038465, PMID:11241532, PMID:11529856, PMID:11879084, PMID:12833394, PMID:15772091, PMID:16841094, PMID:17384684, PMID:18642369, PMID:19381019, PMID:19749790, PMID:25157968, PMID:25606676, PMID:25741868, PMID:26619011, PMID:28492532, PMID:30311386 NCBI chrNW_004936477:21,591,772...21,606,289 JBrowse link
G Pik3ca phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha ISO OMIM NCBI chrNW_004936566:3,924,013...3,951,052 JBrowse link
skin papilloma term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ccl20 C-C motif chemokine ligand 20 ISO protein:decreased expression:skin RGD PMID:21715145 RGD:7483622 NCBI chrNW_004936525:8,238,128...8,240,974 JBrowse link
G Clu clusterin ISO RGD PMID:11085517 RGD:8746700 NCBI chrNW_004936675:499,745...513,515 JBrowse link
G Nrg1 neuregulin 1 ISO DNA:hypermethylation: RGD PMID:31892232 RGD:39456089 NCBI chrNW_004936766:1,104,841...1,306,368 JBrowse link
G Tlr2 toll like receptor 2 ISO protein:increased expression,altered expression:cytoplasm,membrane, nucleus: RGD PMID:24617037 RGD:8553046 NCBI chrNW_004936576:522,234...531,660 JBrowse link
Trichilemmoma term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Hras HRas proto-oncogene, GTPase ISO associated with Nevus sebaceous; DNA:mutation:exon:c.37G>C (p.G13R)(human) RGD PMID:24890286 RGD:12738400 NCBI chrNW_004936888:375,372...378,125 JBrowse link
von Hippel-Lindau disease term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Epas1 endothelial PAS domain protein 1 ISO protein:increased expression:kidney: RGD PMID:22299048 RGD:11041600 NCBI chrNW_004936508:5,855,748...5,938,879 JBrowse link
G Slc18a1 solute carrier family 18 member A1 ISO mRNA:increased expression:tumor (human) RGD PMID:16189177 RGD:5131200 NCBI chrNW_004936555:4,249,821...4,271,379 JBrowse link
G Vhl von Hippel-Lindau tumor suppressor ISO OMIM NCBI chrNW_004936602:3,135,790...3,140,622 JBrowse link
WHIM syndrome term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Cxcr4 C-X-C motif chemokine receptor 4 ISO OMIM NCBI chrNW_004936469:39,794,613...39,798,448 JBrowse link
G Dars1 aspartyl-tRNA synthetase 1 ISO ClinVar Annotator: match by term: Warts, hypogammaglobulinemia, infections, and myelokathexis ClinVar PMID:28492532 NCBI chrNW_004936469:39,921,182...39,979,297 JBrowse link

Term paths to the root
Path 1
Term Annotations click to browse term
  disease 11943
    sensory system disease 4609
      skin disease 2414
        Skin Neoplasms 215
          skin benign neoplasm 48
            Benign Skin Neoplasms, Epithelial + 16
            angiokeratoma of Fordyce + 0
            benign dermal neurilemmoma 0
            clear cell acanthoma 0
            cutaneous fibrous histiocytoma 0
            cutaneous ganglioneuroma 0
            dermis tumor + 1
            dermoid cyst of skin 0
            epidermal appendage tumor 0
            eyelid benign neoplasm + 2
            granular cell tumor + 1
            hair follicle neoplasm + 5
            sebaceous gland neoplasm + 4
            seborrheic keratosis + 3
            skin glomangioma + 0
            skin granular cell tumor 0
            skin hemangioma + 15
            skin lipoma 0
            skin meningioma 0
            sweat gland benign neoplasm + 0
Path 2
Term Annotations click to browse term
  disease 11943
    disease of anatomical entity 11504
      nervous system disease 9435
        sensory system disease 4609
          skin disease 2414
            Skin Neoplasms 215
              skin benign neoplasm 48
                Benign Skin Neoplasms, Epithelial + 16
                angiokeratoma of Fordyce + 0
                benign dermal neurilemmoma 0
                clear cell acanthoma 0
                cutaneous fibrous histiocytoma 0
                cutaneous ganglioneuroma 0
                dermis tumor + 1
                dermoid cyst of skin 0
                epidermal appendage tumor 0
                eyelid benign neoplasm + 2
                granular cell tumor + 1
                hair follicle neoplasm + 5
                sebaceous gland neoplasm + 4
                seborrheic keratosis + 3
                skin glomangioma + 0
                skin granular cell tumor 0
                skin hemangioma + 15
                skin lipoma 0
                skin meningioma 0
                sweat gland benign neoplasm + 0
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.