SOX1

SRY-box transcription factor 1, the group of SRY-box transcription factors

Basic information

Region (hg38): 13:112067149-112071706

Links

ENSG00000182968 ∙ NCBI:6656 ∙ OMIM:602148 ∙ HGNC:11189 ∙ Uniprot:O00570 ∙ 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 SOX1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SOX1 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				5	3	8
missense			25			25
nonsense						0
start loss						0
frameshift						0
inframe indel				4	1	5
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	9	4

Variants in SOX1

This is a list of pathogenic ClinVar variants found in the SOX1 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-112067678-A-C		not specified	Uncertain significance (Apr 25, 2023)
13-112067685-C-T			Benign (Jul 23, 2018)
13-112067705-C-T		not specified	Uncertain significance (Jan 03, 2024)
13-112067739-G-C		SOX1-related disorder	Likely benign (Nov 17, 2020)
13-112067742-G-C		SOX1-related disorder	Likely benign (Nov 17, 2020)
13-112067770-G-A		not specified	Uncertain significance (Apr 22, 2022)
13-112067772-CGGCGGCGGCGGG-C		SOX1-related disorder	Likely benign (Mar 09, 2021)
13-112067785-G-T		not specified	Uncertain significance (Jun 07, 2024)
13-112067786-G-A		not specified	Uncertain significance (Oct 06, 2021)
13-112068036-C-T			Benign (Dec 31, 2019)
13-112068041-C-T		not specified	Uncertain significance (Aug 09, 2021)
13-112068046-C-T		not specified	Uncertain significance (Jun 17, 2024)
13-112068140-T-C		not specified	Uncertain significance (Mar 21, 2022)
13-112068181-G-A		not specified	Uncertain significance (Sep 26, 2023)
13-112068205-C-T		not specified	Uncertain significance (Sep 17, 2021)
13-112068207-C-A		not specified	Uncertain significance (Mar 27, 2024)
13-112068323-C-G		not specified	Uncertain significance (Mar 30, 2024)
13-112068326-A-C		not specified	Uncertain significance (Nov 02, 2021)
13-112068332-A-C		not specified	Uncertain significance (Nov 02, 2021)
13-112068338-A-C		not specified	Uncertain significance (Jan 10, 2022)
13-112068343-GCGCACC-G			Likely benign (Jan 01, 2023)
13-112068362-A-C		not specified	Uncertain significance (Aug 10, 2021)
13-112068370-G-GCGCACC		SOX1-related disorder	Benign (Oct 31, 2019)
13-112068394-A-G		not specified	Uncertain significance (May 02, 2024)
13-112068446-A-G		not specified	Uncertain significance (Aug 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SOX1	protein_coding	protein_coding	ENST00000330949	1	4108

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.623	0.348	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.578	71	86.1	0.825	0.00000405	2443
Missense in Polyphen		18	46.188	0.38972		595
Synonymous	-1.96	54	38.5	1.40	0.00000185	846
Loss of Function	1.63	0	3.11	0.00	1.32e-7	89

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: Transcriptional activator. May function as a switch in neuronal development. Keeps neural cells undifferentiated by counteracting the activity of proneural proteins and suppresses neuronal differentiation (By similarity). {ECO:0000250}.
• Pathway: Cardiac Progenitor Differentiation;Wnt Signaling Pathway;Wnt (Consensus)

Haploinsufficiency Scores

• pHI: 0.185

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.341

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sox1
• Phenotype: cellular phenotype; muscle phenotype; growth/size/body region phenotype; embryo phenotype; immune system phenotype; vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: neuron migration;lens morphogenesis in camera-type eye;chromatin organization;regulation of transcription, DNA-templated;central nervous system development;ventral spinal cord interneuron specification;forebrain neuron development;cell differentiation;neuron differentiation;positive regulation of transcription by RNA polymerase II;cellular response to leukemia inhibitory factor
• 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 transcription activator activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;protein binding