SOX15

SRY-box transcription factor 15, the group of SRY-box transcription factors

Basic information

Region (hg38): 17:7588178-7590094

Previous symbols: [ "SOX20" ]

Links

ENSG00000129194 ∙ NCBI:6665 ∙ OMIM:601297 ∙ HGNC:11196 ∙ Uniprot:O60248 ∙ 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 SOX15 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SOX15 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			17	2		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	18	2	0

Variants in SOX15

This is a list of pathogenic ClinVar variants found in the SOX15 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-7588203-C-T		MPDU1-congenital disorder of glycosylation	Uncertain significance (Jan 13, 2018)
17-7588403-G-A		not specified	Uncertain significance (Aug 01, 2022)
17-7588454-T-A		not specified	Uncertain significance (Dec 07, 2021)
17-7588473-G-T		not specified	Uncertain significance (May 23, 2024)
17-7588476-C-G		not specified	Uncertain significance (Jun 06, 2023)
17-7588506-G-A		not specified	Uncertain significance (Dec 12, 2024)
17-7588511-C-G		not specified	Uncertain significance (Feb 06, 2023)
17-7588514-G-A		not specified	Uncertain significance (Jun 24, 2022)
17-7588529-A-G		not specified	Likely benign (Mar 14, 2023)
17-7589169-T-C		not specified	Uncertain significance (Feb 10, 2022)
17-7589240-G-A		not specified	Uncertain significance (Jul 22, 2024)
17-7589248-G-T		not specified	Uncertain significance (Jun 30, 2024)
17-7589280-G-T		not specified	Uncertain significance (Jun 16, 2023)
17-7589321-C-T		not specified	Uncertain significance (Sep 21, 2023)
17-7589397-C-G		not specified	Uncertain significance (Apr 08, 2024)
17-7589403-C-T		not specified	Uncertain significance (Jun 02, 2023)
17-7589469-G-T		not specified	Uncertain significance (Jun 16, 2024)
17-7589558-G-A		not specified	Likely benign (Jun 01, 2023)
17-7589616-C-A		not specified	Uncertain significance (Oct 07, 2024)
17-7589630-G-A		not specified	Uncertain significance (Jun 11, 2021)
17-7589672-G-T		not specified	Uncertain significance (Nov 16, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SOX15	protein_coding	protein_coding	ENST00000250055	2	1993

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.215	0.750	125120	0	2	125122	0.00000799

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.622	109	129	0.846	0.00000643	1444
Missense in Polyphen		31	45.497	0.68136		519
Synonymous	0.556	52	57.4	0.907	0.00000292	506
Loss of Function	1.76	2	7.03	0.285	3.04e-7	82

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)	0.00000885	0.00000884
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds to the 5'-AACAAT-3' sequence.

Haploinsufficiency Scores

• pHI: 0.155
• hipred: N
• hipred_score: 0.238
• ghis: 0.554

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.737

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sox15
• Phenotype: muscle phenotype; normal phenotype

Zebrafish Information Network

• Gene name: sox19b
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: kinked

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;chromatin organization;regulation of transcription, DNA-templated;regulation of transcription by RNA polymerase II;central nervous system development;male gonad development;positive regulation of satellite cell activation involved in skeletal muscle regeneration;cell differentiation;neuron differentiation;skeletal muscle tissue regeneration;negative regulation of striated muscle tissue development;positive regulation of transcription by RNA polymerase II;myoblast development;positive regulation of G0 to G1 transition;positive regulation of myoblast proliferation
• Cellular component: nucleus;cytoplasm;nuclear transcription factor complex
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;chromatin binding;DNA-binding transcription factor activity;protein binding;protein heterodimerization activity