Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) RatMine GViewer (Genome Viewer) Overgo Probe Designer ACP Haplotyper Genome Scanner VCMap
Aging & Age-Related Disease Cancer Cardiovascular Disease COVID-19 Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models PhenoMiner (Quantitative Phenotypes) Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes GERRC (Gene Editing Rat Resource Center) Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Poster Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources

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:hypospadias
go back to main search page
Accession:DOID:10892 term browser browse the term
Definition:A birth defect due to malformation of the URETHRA in which the urethral opening is below its normal location. In the male, the malformed urethra generally opens on the ventral surface of the PENIS or on the PERINEUM. In the female, the malformed urethral opening is in the VAGINA.
Synonyms:exact_synonym: HYSP4;   familial hypospadias;   hypospadia
 related_synonym: Hypospadias 4, X-Linked, Susceptibility to
 primary_id: MESH:D007021
 alt_id: OMIM:300856;   RDO:0000276;   RDO:0010084
 xref: ICD10CM:Q54;   ICD10CM:Q54.9;   NCI:C40341;   OMIM:PS300633;   ORDO:440
For additional species annotation, visit the Alliance of Genome Resources.

show annotations for term's descendants           Sort by:
 
hypospadias term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ar androgen receptor ISO
ISS		 OMIM:146450 | OMIM:300633 | OMIM:300758 | OMIM:300856
mRNA:decreased expression:mucosa of urethra 		MouseDO PMID:15472213, PMID:23386417 RGD:1578685, RGD:11576230 NCBI chr  X:67,656,253...67,828,998
Ensembl chr  X:67,656,253...67,829,026 		JBrowse link
G Atf3 activating transcription factor 3 ISO CTD Direct Evidence: marker/mechanism CTD PMID:18001166 NCBI chr13:109,817,892...109,849,632
Ensembl chr13:109,817,728...109,849,632 		JBrowse link
G Cyp1a1 cytochrome P450, family 1, subfamily a, polypeptide 1 no_association ISO RGD PMID:15579657, PMID:21300689 RGD:11576312, RGD:11576313 NCBI chr 8:62,472,087...62,478,122
Ensembl chr 8:62,472,095...62,478,147 		JBrowse link
G Dgkk diacylglycerol kinase kappa ISO CTD Direct Evidence: marker/mechanism CTD PMID:21113153 PMID:27098078 NCBI chr  X:16,441,318...16,526,046
Ensembl chr  X:16,442,899...16,537,888 		JBrowse link
G Esr2 estrogen receptor 2 susceptibility ISO DNA:snps, repeat:promoter, 3' utr:rs2987983, rs10483774, g.dupCA (rs1256062) (human) RGD PMID:17579196, PMID:17579196 RGD:1626506, RGD:1626506 NCBI chr 6:99,163,953...99,214,711
Ensembl chr 6:99,164,357...99,214,251 		JBrowse link
G Fgf10 fibroblast growth factor 10 IEP RGD PMID:19464577 RGD:2314151 NCBI chr 2:51,673,480...51,747,533
Ensembl chr 2:51,672,722...51,750,369 		JBrowse link
G Fgf8 fibroblast growth factor 8 IEP RGD PMID:19464577 RGD:2314151 NCBI chr 1:265,492,949...265,498,965
Ensembl chr 1:265,493,124...265,498,831 		JBrowse link
G Fgfr2 fibroblast growth factor receptor 2 IEP mRNA:decreased expression:male genital tubercle (rat) RGD PMID:19464577 RGD:2314151 NCBI chr 1:200,590,951...200,696,946
Ensembl chr 1:200,590,953...200,696,928 		JBrowse link
G Gli3 GLI family zinc finger 3 IEP mRNA:decreased expression:male genital tubercle RGD PMID:27079746 RGD:12743602 NCBI chr17:52,294,942...52,569,036
Ensembl chr17:52,294,942...52,569,036 		JBrowse link
G Gstm1 glutathione S-transferase mu 1 ISO DNA:deletion, haplotype: : (human) RGD PMID:21300689 RGD:11576313 NCBI chr 2:210,803,869...210,809,461
Ensembl chr 2:210,803,869...210,809,306 		JBrowse link
G Gstt1 glutathione S-transferase theta 1 ISO DNA:deletion, haplotype: : (human) RGD PMID:21300689 RGD:11576313 NCBI chr20:13,799,102...13,816,527
Ensembl chr20:13,799,102...13,816,526 		JBrowse link
G Hhip Hedgehog-interacting protein ISO CTD Direct Evidence: marker/mechanism CTD PMID:31568847 NCBI chr19:31,525,134...31,614,487
Ensembl chr19:31,524,671...31,614,246 		JBrowse link
G Hoxa13 homeo box A13 IEP mRNA:decreased expression:male genital tubercle RGD PMID:27079746 RGD:12743602 NCBI chr 4:82,313,383...82,315,550
Ensembl chr 4:82,228,017...82,229,397 		JBrowse link
G Hoxd13 homeo box D13 IEP mRNA:decreased expression:male genital tubercle RGD PMID:27079746 RGD:12743602 NCBI chr 3:61,590,376...61,593,692
Ensembl chr 3:61,590,376...61,593,692 		JBrowse link
G Hsd3b1 hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1 ISO DNA:point mutation:CDS:heterozygous S213T or S284R, result in decreased enzyme activity RGD PMID:14764821 RGD:1625114
G Hsd3b2 hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 2 ISO CTD Direct Evidence: marker/mechanism CTD PMID:14764821 NCBI chr 2:200,712,895...200,722,429
Ensembl chr 2:202,341,422...202,350,929 		JBrowse link
G Srd5a2 steroid 5 alpha-reductase 2 susceptibility ISO protein:missense mutations:cds:p.R227Q, p.F186L (human) RGD PMID:10514539 RGD:1600059 NCBI chr 6:25,279,635...25,315,501
Ensembl chr 6:25,279,626...25,315,511 		JBrowse link
Guttmacher syndrome term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Hoxa13 homeo box A13 ISO CTD Direct Evidence: marker/mechanism
ClinVar Annotator: match by OMIM:176305		 OMIM
CTD
ClinVar		 PMID:8484413 PMID:11968094 PMID:24239177 NCBI chr 4:82,313,383...82,315,550
Ensembl chr 4:82,228,017...82,229,397 		JBrowse link
Hypospadias 1, X-Linked term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Ar androgen receptor ISO ClinVar Annotator: match by term: Hypospadias 1, X-linked
ClinVar Annotator: match by OMIM:300633		 OMIM
ClinVar		 PMID:8097257 PMID:8683794 PMID:25326637 PMID:25741868 NCBI chr  X:67,656,253...67,828,998
Ensembl chr  X:67,656,253...67,829,026 		JBrowse link
Opitz GBBB syndrome type I term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Mid1 midline 1 ISO ClinVar Annotator: match by term: Opitz GBBB syndrome, type I
ClinVar Annotator: match by term: OPITZ-G SYNDROME, TYPE I		 OMIM
ClinVar		 PMID:9354791 PMID:11030761 PMID:12545276 PMID:15558842 PMID:17221865 PMID:18360914 PMID:18949047 PMID:21326312 PMID:23757202 PMID:25207814 PMID:25741868 PMID:25874572 PMID:28492532 NCBI chr  X:25,458,782...25,839,941
Ensembl chr  X:25,458,771...25,628,272 		JBrowse link
Opitz GBBB syndrome type II term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Specc1l sperm antigen with calponin homology and coiled-coil domains 1-like ISO ClinVar Annotator: match by term: Opitz GBBB syndrome, type II OMIM
ClinVar		 PMID:3228142 PMID:25412741 PMID:25741868 NCBI chr20:14,287,470...14,393,879
Ensembl chr20:14,287,457...14,393,793 		JBrowse link
Opitz-GBBB syndrome term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Mid1 midline 1 ISS
ISO		 OMIM:145410 | OMIM:300000
ClinVar Annotator: match by term: TELECANTHUS-HYPOSPADIAS SYNDROME		 MouseDO
ClinVar		 PMID:25741868 PMID:28492532 NCBI chr  X:25,458,782...25,839,941
Ensembl chr  X:25,458,771...25,628,272 		JBrowse link
Pseudovaginal Perineoscrotal Hypospadias term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Cyp1b1 cytochrome P450, family 1, subfamily b, polypeptide 1 ISO ClinVar Annotator: match by term: Familial incomplete male pseudohermaphroditism, type 2 ClinVar PMID:11403040 PMID:12036985 PMID:19643970 PMID:22004014 PMID:23218701 PMID:23922489 PMID:24033266 PMID:24281366 PMID:25741868 PMID:27820421 PMID:28492532 PMID:32499604 NCBI chr 6:2,308,179...2,316,739
Ensembl chr 6:2,307,808...2,316,722 		JBrowse link
G Srd5a2 steroid 5 alpha-reductase 2 ISO ClinVar Annotator: match by OMIM:264600
CTD Direct Evidence: marker/mechanism
ClinVar Annotator: match by term: 3-Oxo-5 alpha-steroid delta 4-dehydrogenase deficiency		 OMIM
ClinVar
CTD		 PMID:431680 PMID:835597 PMID:1406794 PMID:1522235 PMID:1944596 PMID:2154055 PMID:2665940 PMID:7554313 PMID:7608269 PMID:8110760 PMID:8262007 PMID:8626825 PMID:8706317 PMID:8723114 PMID:8768837 PMID:8784107 PMID:9066886 PMID:9135696 PMID:9208814 PMID:9467575 PMID:9745434 PMID:9843052 PMID:10501358 PMID:10718838 PMID:10898110 PMID:10999800 PMID:11869378 PMID:12576851 PMID:12843198 PMID:14560315 PMID:14594182 PMID:15064320 PMID:15266301 PMID:15528927 PMID:15770495 PMID:17609295 PMID:18097518 PMID:18314109 PMID:18350250 PMID:18384427 PMID:18391525 PMID:18469342 PMID:18717241 PMID:19342739 PMID:19492581 PMID:20019388 PMID:20190539 PMID:20493473 PMID:20583543 PMID:20736251 PMID:21147889 PMID:21402750 PMID:21540559 PMID:21631525 PMID:22272144 PMID:22453073 PMID:22876553 PMID:23329752 PMID:23633205 PMID:24665940 PMID:24737579 PMID:24885102 PMID:25605705 PMID:25741868 PMID:25899528 PMID:26446026 PMID:26980298 PMID:27070133 PMID:27899157 PMID:28492532 PMID:28544750 PMID:28663096 PMID:31186340 PMID:288959874 NCBI chr 6:25,279,635...25,315,501
Ensembl chr 6:25,279,626...25,315,511 		JBrowse link
scalp-ear-nipple syndrome term browser
Symbol Object Name Qualifiers Evidence Notes Source PubMed Reference(s) RGD Reference(s) Position
G Kctd1 potassium channel tetramerization domain containing 1 ISO ClinVar Annotator: match by term: Scalp-ear-nipple syndrome
ClinVar Annotator: match by OMIM:181270		 OMIM
ClinVar		 PMID:1799422 PMID:8042668 PMID:9383029 PMID:10517259 PMID:16411189 PMID:23541344 PMID:25741868 NCBI chr18:6,374,778...6,474,990
Ensembl chr18:6,374,778...6,474,990 		JBrowse link
Term paths to the root
Path 1
Term Annotations click to browse term
  disease 16909
    physical disorder 2917
      hypospadias 21
        Anal Atresia, Hypospadias, and Penoscrotal Inversion 0
        Guttmacher syndrome 1
        Hypospadias 1, X-Linked 1
        Hypospadias 2, X-Linked 0
        Hypospadias 3, Autosomal 0
        Hypospadias, Hypertelorism, Upper Lid Coloboma, and Mixed-Type Hearing Loss 0
        Hypospadias-Mental Retardation Syndrome 0
        Naguib-Richieri-Costa Syndrome 0
        Opitz-GBBB syndrome + 2
        Pseudovaginal Perineoscrotal Hypospadias 2
        Radial Hypoplasia, Triphalangeal Thumbs and Hypospadias 0
        Radius Absent Anogenital Anomalies 0
        Schilbach-Rott Syndrome 0
        Stratton-Parker Syndrome 0
        scalp-ear-nipple syndrome 1
Path 2
Term Annotations click to browse term
  disease 16909
    disease of anatomical entity 16281
      Urogenital Diseases 4199
        reproductive system disease 2606
          male reproductive system disease 1791
            penile disease 62
              hypospadias 21
                Anal Atresia, Hypospadias, and Penoscrotal Inversion 0
                Guttmacher syndrome 1
                Hypospadias 1, X-Linked 1
                Hypospadias 2, X-Linked 0
                Hypospadias 3, Autosomal 0
                Hypospadias, Hypertelorism, Upper Lid Coloboma, and Mixed-Type Hearing Loss 0
                Hypospadias-Mental Retardation Syndrome 0
                Naguib-Richieri-Costa Syndrome 0
                Opitz-GBBB syndrome + 2
                Pseudovaginal Perineoscrotal Hypospadias 2
                Radial Hypoplasia, Triphalangeal Thumbs and Hypospadias 0
                Radius Absent Anogenital Anomalies 0
                Schilbach-Rott Syndrome 0
                Stratton-Parker Syndrome 0
                scalp-ear-nipple syndrome 1
paths to the root