SOX13

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

Basic information

Region (hg38): 1:204073114-204127743

Links

ENSG00000143842 ∙ NCBI:9580 ∙ OMIM:604748 ∙ HGNC:11192 ∙ Uniprot:Q9UN79 ∙ 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 SOX13 gene.

• Inborn genetic diseases (20 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SOX13 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			19	1		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	1	0

Variants in SOX13

This is a list of pathogenic ClinVar variants found in the SOX13 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-204112935-T-A		not specified	Uncertain significance (May 30, 2023)
1-204112941-C-T		not specified	Uncertain significance (Oct 27, 2022)
1-204113018-G-A		not specified	Uncertain significance (Feb 06, 2023)
1-204113072-C-T		not specified	Uncertain significance (Oct 03, 2022)
1-204113075-G-A		not specified	Uncertain significance (Jan 24, 2024)
1-204114323-C-A		not specified	Uncertain significance (Mar 11, 2022)
1-204114339-G-T		not specified	Uncertain significance (Nov 17, 2023)
1-204114394-G-T		not specified	Uncertain significance (Apr 11, 2023)
1-204114418-G-A		not specified	Uncertain significance (Apr 07, 2023)
1-204116621-C-T		not specified	Uncertain significance (Nov 23, 2021)
1-204116674-G-C		not specified	Uncertain significance (Sep 20, 2023)
1-204117128-A-G		not specified	Uncertain significance (Feb 28, 2024)
1-204117159-A-G		not specified	Uncertain significance (Dec 27, 2022)
1-204117650-C-T		not specified	Uncertain significance (Dec 07, 2023)
1-204121925-C-G		not specified	Uncertain significance (Jan 17, 2024)
1-204121964-G-A		not specified	Uncertain significance (Dec 16, 2023)
1-204122336-C-T		not specified	Uncertain significance (Dec 15, 2022)
1-204122358-C-T		not specified	Uncertain significance (Dec 20, 2022)
1-204122361-C-T		not specified	Uncertain significance (May 31, 2023)
1-204122917-G-A		not specified	Uncertain significance (Nov 09, 2021)
1-204123114-C-G		not specified	Uncertain significance (Sep 12, 2023)
1-204123149-G-A		not specified	Uncertain significance (May 27, 2022)
1-204123202-A-G		not specified	Likely benign (Dec 14, 2021)
1-204123798-A-G		not specified	Uncertain significance (Jul 05, 2023)
1-204124695-A-C		not specified	Uncertain significance (Sep 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SOX13	protein_coding	protein_coding	ENST00000367204	13	54621

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.942	0.0582	124665	0	6	124671	0.0000241

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.74	270	363	0.743	0.0000208	4044
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000871	0.0000871
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000886	0.00000885
Middle Eastern	0.00	0.00
South Asian	0.0000654	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds to the sequence 5'-AACAAT-3'. {ECO:0000250}.
• Pathway: Signaling by WNT;Signal Transduction;Deactivation of the beta-catenin transactivating complex;TCF dependent signaling in response to WNT (Consensus)

Recessive Scores

• pRec: 0.147

Intolerance Scores

• loftool: 0.116
• rvis_EVS: 0.75
• rvis_percentile_EVS: 86.71

Haploinsufficiency Scores

• pHI: 0.258
• hipred: N
• hipred_score: 0.485
• ghis: 0.481

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.826

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sox13
• Phenotype: growth/size/body region phenotype; hematopoietic system phenotype; immune system phenotype

Gene ontology

• 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
• Cellular component: nucleus;nucleoplasm
• 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