SOX13

protein-coding

SRY-box transcription factor 13, the group of SRY-box transcription factors

Gene summary

This gene encodes a member of the SOX (SRY-related HMG-box) family of transcription factors involved in the regulation of embryonic development and in the determination of cell fate. The encoded protein may act as a transcriptional regulator after forming a protein complex with other proteins. It has also been determined to be a type-1 diabetes autoantigen, also known as islet cell antibody 12. [provided by RefSeq, Jul 2008]

MANE transcript

NM_005686.3

Inheritance

—

ClinVar variants

U:94B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.16

Max pathogenic AF

—

Genomic locus

chr1:204,073,115-204,127,743

External References & Databases

Ensembl (ENSG00000143842)

Transcript & Mutation Effects

hg38 • Region Span ~54.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SOX13 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 84

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005686.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	1 clinvar		2
missense			85 clinvar	1 clinvar		86
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			6 clinvar			6
Total	0	0	94	2	0	96

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 38 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005686.3	RefSeq	NP_005677.2	13	MANE Select
ENST00000367204.6	Ensembl	ENSP00000356172.1	13	MANE Select
ENST00000480326.1	Ensembl	ENSP00000434093.1	4	Standard
ENST00000525442.1	Ensembl	ENSP00000433595.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Signaling by WNT
Signal Transduction
Deactivation of the beta-catenin transactivating complex
TCF dependent signaling in response to WNT

Biological Process

anatomical structure morphogenesis
cell fate commitment
regulation of gamma-delta T cell differentiation
negative regulation of transcription, DNA-templated
positive regulation of transcription by RNA polymerase II

Molecular Function

RNA polymerase II regulatory region sequence-specific DNA binding
DNA-binding transcription factor activity, RNA polymerase II-specific
DNA-binding transcription factor activity
protein binding
sequence-specific DNA binding

Cellular Component

nucleus
nucleoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000367204
Coding exons: 13
Length: 54621
Individuals with no LoFs: 124665
Homozygous LoFs: 0
Heterozygous LoFs: 6
Defined: 124671
p: 0.0000241

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.74	270	363	0.743	0.0000208	4044
Missense (PolyPhen)		76	129.79	0.58558		1362
Synonymous	0.426	140	147	0.955	0.00000856	1199
Loss of Function	4.33	5	31.0	0.161	0.00000160	335

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000089	0.0000088	rare
South Asian	0.000065	0.000065	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Binds to the sequence 5'-AACAAT-3'. {ECO:0000250}.;

Recessive Scores

pRec: 0.147

Intolerance Scores

LoFtool: 0.116
RVIS EVS: 0.75
RVIS percentile EVS: 86.71

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.826

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium