RGD:40888268 Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease 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 Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes 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 Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources

Variant: RGD:40888268 -  Homo sapiens

RGD ID: 40888268
RS ID: rs1714842576
ClinVar ID: CV974914
Genic Status: GENIC
Type: SNV (SO:0001483) 
Associated Genes: LOC108281177  SOX2  SOX2-OT  
Reference Nucleotide: C
Variant Nucleotide: G
Position
Assembly Chr Position
GRCh37 3 181,430,279
GRCh38 3 181,712,491
JBrowse: View Region in Genome Browser (JBrowse)
Model



ClinVar Data
HGVS Name(s) Last Evaluated Molecular Consequence Clinical Significance Trait Synonyms
NM_003106.4:c.131C>G
LRG_719:g.5558C>G
NG_009080.1:g.5558C>G
NC_000003.12:g.181712491C>G
More... 		missense variant pathogenic AEG syndrome; Anophthalmia clinical with associated anomalies; Anophthalmia esophageal genital syndrome; Anophthalmia microphthalmia esophageal atresia; Microphthalmia and esophageal atresia syndrome; Microphthalmia syndromic 3
Disease Annotations     Click to see Annotation Detail View


Variant Details
Variant Transcripts
Gene Symbol:SOX2
Accession:NM_003106
Location:EXON
Amino Acid Prediction: P to R (nonsynonymous)
Amino Acid Position: 44
Amino Acid Sequence
(Calculated using NCBI transcript definition)
MYNMMETELKPPGPQQTSGGGGGNSTAAAAGGNQKNSPDRVKRRMNAFMVWSRGQRRKMAQENPKMHNSEISKRLGAEWK
LLSETEKRPFIDEAKRLRALHMKEHPDYKYRPRRKTKTLMKKDKYTLPGGLLAPGGNSMASGVGVGAGLGAGVNQRMDSY
AHMNGWSNGSYSMMQDQLGYPQHPGLNAHGAAQMQPMHRYDVSALQYNSMTSSQTYMNGSPTYSMSYSQQGTPGMALGSM
GSVVKSEASSSPPVVTSSSHSRAPCQAGDLRDMISMYLPGAEVPEPAAPSRLHMSQHYQSGPVPGTAINGTLPLSHM*

Gene Symbol:SOX2-OT
Accession:NR_075092
Location:INTRON;NON-CODING

Gene Symbol:SOX2-OT
Accession:NR_075089
Location:INTRON;NON-CODING

Gene Symbol:SOX2-OT
Accession:NR_075090
Location:INTRON;NON-CODING

Gene Symbol:SOX2-OT
Accession:NR_004053
Location:INTRON;NON-CODING

Gene Symbol:SOX2-OT
Accession:NR_075091
Location:INTRON;NON-CODING

Gene Symbol:SOX2-OT
Accession:NR_075093
Location:INTRON;NON-CODING

Variant Samples

Additional Information

Database Acc Id Source(s)
ClinVar RCV001267854 CLINVAR
dbSNP (RS) rs1714842576 CLINVAR
MedGen C1859773 CLINVAR
NCBI Gene LOC108281177 CLINVAR
  SOX2 CLINVAR
  SOX2-OT CLINVAR
OMIM 184429 CLINVAR
  206900 CLINVAR
  616338 CLINVAR