SOX2-OT

SOX2 overlapping transcript, the group of Overlapping transcripts

Basic information

Region (hg38): 3:180989510-181836880

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						0
non coding	65	12	49	34	11	171
Total	65	12	49	34	11

Highest pathogenic variant AF is 0.00000659

Variants in SOX2-OT

This is a list of pathogenic ClinVar variants found in the SOX2-OT region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-180989584-G-A		not specified • 3-methylglutaconic aciduria type 5	Likely benign (Jan 28, 2024)
3-180989587-A-G		3-methylglutaconic aciduria type 5	Likely benign (Nov 06, 2020)
3-180989601-A-G		3-methylglutaconic aciduria type 5	Uncertain significance (Feb 06, 2022)
3-180989602-T-C		3-methylglutaconic aciduria type 5	Uncertain significance (Aug 27, 2021)
3-180989631-C-A		not specified • DNAJC19-related disorder	Benign (Feb 14, 2013)
3-181712324-C-T			Benign (Mar 03, 2015)
3-181712330-C-T		not specified	Benign (May 26, 2015)
3-181712336-GGCCGGGCCCGCGCACAGCGCCCGCATGTACAACATGATGGAGACGGAGCTGAAGCC-G		Anophthalmia/microphthalmia-esophageal atresia syndrome	Pathogenic (-)
3-181712341-G-T			Likely benign (Apr 26, 2018)
3-181712350-A-C			Likely benign (Mar 23, 2018)
3-181712362-T-TG		Anophthalmia/microphthalmia-esophageal atresia syndrome	Pathogenic (Dec 19, 2019)
3-181712376-G-T		Anophthalmia/microphthalmia-esophageal atresia syndrome	Pathogenic (-)
3-181712380-C-T		Congenital aniridia	Uncertain significance (Apr 17, 2020)
3-181712381-G-C		Anophthalmia/microphthalmia-esophageal atresia syndrome	Uncertain significance (Oct 05, 2023)
3-181712382-G-T		Anophthalmia/microphthalmia-esophageal atresia syndrome	Likely pathogenic (Nov 26, 2020)
3-181712384-GC-G		Anophthalmia/microphthalmia-esophageal atresia syndrome	Pathogenic (Dec 22, 2022)
3-181712393-G-T		Anophthalmia/microphthalmia-esophageal atresia syndrome • SOX2-related disorder	Likely benign (Jun 18, 2017)
3-181712399-C-A		Anophthalmia/microphthalmia-esophageal atresia syndrome	Likely benign (Dec 18, 2022)
3-181712402-G-T			Likely benign (Feb 05, 2021)
3-181712405-G-A		Anophthalmia/microphthalmia-esophageal atresia syndrome	Likely benign (Jan 06, 2024)
3-181712411-T-C			Likely benign (Jul 31, 2018)
3-181712412-TC-AA		Anophthalmia/microphthalmia-esophageal atresia syndrome	Conflicting classifications of pathogenicity (Jan 02, 2024)
3-181712413-C-A		Anophthalmia/microphthalmia-esophageal atresia syndrome	Pathogenic (Dec 19, 2019)
3-181712413-CG-C		Anophthalmia/microphthalmia-esophageal atresia syndrome	Pathogenic (-)
3-181712413-C-CG		Anophthalmia/microphthalmia-esophageal atresia syndrome	Pathogenic (Sep 03, 2021)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

Mouse Genome Informatics

• Gene name: Sox2ot