SOX21

SRY-box transcription factor 21, the group of SRY-box transcription factors

Basic information

Region (hg38): 13:94709622-94712545

Links

ENSG00000125285 ∙ NCBI:11166 ∙ OMIM:604974 ∙ HGNC:11197 ∙ Uniprot:Q9Y651 ∙ AlphaFold ∙ 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 SOX21 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SOX21 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					1	1
missense			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	1

Variants in SOX21

This is a list of pathogenic ClinVar variants found in the SOX21 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-94711233-C-T		not specified	Uncertain significance (May 15, 2024)
13-94711245-G-A		not specified	Uncertain significance (Mar 31, 2024)
13-94711270-C-T		not specified	Uncertain significance (Jan 18, 2022)
13-94711299-G-A		not specified	Uncertain significance (Jul 13, 2022)
13-94711319-G-A		not specified	Uncertain significance (Jan 04, 2024)
13-94711365-G-A		not specified	Uncertain significance (Jul 14, 2023)
13-94711388-C-T		not specified	Uncertain significance (Dec 21, 2023)
13-94711439-G-T		not specified	Uncertain significance (Apr 18, 2023)
13-94711461-A-T		not specified	Uncertain significance (Nov 20, 2024)
13-94711470-A-G		not specified	Uncertain significance (Feb 03, 2022)
13-94711493-G-C		not specified	Uncertain significance (Feb 05, 2024)
13-94711506-T-G		not specified	Uncertain significance (Jan 03, 2024)
13-94711613-G-T		not specified	Uncertain significance (Oct 08, 2024)
13-94711650-G-A		not specified	Uncertain significance (Feb 07, 2023)
13-94711745-C-G		not specified	Uncertain significance (Mar 30, 2024)
13-94711792-C-G			Benign (Oct 13, 2020)
13-94711896-A-C		not specified	Uncertain significance (Mar 30, 2024)
13-94711901-G-C		not specified	Uncertain significance (Mar 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SOX21	protein_coding	protein_coding	ENST00000376945	1	2504

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.713	0.273	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.74	55	105	0.522	0.00000485	1716
Missense in Polyphen		22	53.403	0.41196		656
Synonymous	1.89	32	48.8	0.655	0.00000240	592
Loss of Function	1.88	0	4.12	0.00	1.75e-7	70

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role as an activator of transcription of OPRM1. {ECO:0000250}.
• Pathway: Mesodermal Commitment Pathway (Consensus)

Haploinsufficiency Scores

• pHI: 0.689
• ghis: 0.645

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.163

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sox21
• Phenotype: endocrine/exocrine gland phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: sox21b
• Affected structure: lens
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;hair follicle development;regulation of transcription, DNA-templated;regulation of transcription by RNA polymerase II;central nervous system development;cell differentiation;neuron differentiation;positive regulation of transcription by RNA polymerase II;stem cell differentiation
• Cellular component: cellular_component;nucleus;nuclear transcription factor complex
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity