SOX2-OT

SOX2 overlapping transcript, the group of Overlapping transcripts

Basic information

Previous symbols: [ "SOX2OT" ]

Links

ENSG00000242808

∙ NCBI:347689 ∙ OMIM:616338 ∙ HGNC:20209 ∙ ∙ ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SOX2-OT gene.

Anophthalmia/microphthalmia-esophageal atresia syndrome (106 variants)
not provided (65 variants)
Inborn genetic diseases (11 variants)
not specified (6 variants)
SOX2-related condition (2 variants)
Optic nerve hypoplasia and abnormalities of the central nervous system (2 variants)
Anophthalmia (2 variants)
Developmental disorder (1 variants)
Septo-optic dysplasia sequence (1 variants)
Congenital aniridia (1 variants)
SOX2-Related Disorder (1 variants)
Amenorrhea (1 variants)
Chorioretinal coloboma (1 variants)
Microphthalmia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SOX2-OT gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region ? Intron variants in splice region, excluding donor/acceptor (+/-2bp)						0
non coding ? UTR, intron and other, non coding variants	65 clinvar	12 clinvar	49 clinvar	34 clinvar	11 clinvar	171
Total	65	12	49	34	11

Highest pathogenic variant AF is 0.00000659

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

Mouse Genome Informatics

Gene name: Sox2ot
Phenotype