SOX14

SRY-box transcription factor 14, the group of SRY-box transcription factors

Basic information

Region (hg38): 3:137764315-137766334

Links

ENSG00000168875 ∙ NCBI:8403 ∙ OMIM:604747 ∙ HGNC:11193 ∙ Uniprot:O95416 ∙ 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 SOX14 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SOX14 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			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	0	0

Variants in SOX14

This is a list of pathogenic ClinVar variants found in the SOX14 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-137764845-G-A		not specified	Uncertain significance (Jan 03, 2024)
3-137764917-G-A		not specified	Uncertain significance (Jan 26, 2022)
3-137764941-G-A		not specified	Uncertain significance (Feb 13, 2024)
3-137765112-C-A		not specified	Uncertain significance (Aug 01, 2024)
3-137765160-C-T		not specified	Uncertain significance (May 14, 2024)
3-137765226-G-T		not specified	Uncertain significance (May 18, 2022)
3-137765302-A-G		not specified	Uncertain significance (Aug 11, 2024)
3-137765316-G-A		not specified	Uncertain significance (Dec 18, 2023)
3-137765337-C-G		not specified	Uncertain significance (Oct 06, 2022)
3-137765406-T-C		not specified	Uncertain significance (Jan 31, 2024)
3-137765470-T-G		not specified	Uncertain significance (Dec 13, 2023)
3-137765503-T-C		not specified	Uncertain significance (Apr 25, 2022)
3-137765505-TA-T		Anophthalmia-microphthalmia syndrome	Likely benign (Jan 01, 2013)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SOX14	protein_coding	protein_coding	ENST00000306087	1	818

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.856	0.142	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.14	107	146	0.734	0.00000655	1543
Missense in Polyphen		27	52.642	0.5129		559
Synonymous	0.100	65	66.0	0.984	0.00000304	504
Loss of Function	2.33	0	6.35	0.00	2.74e-7	73

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: Acts as a negative regulator of transcription. {ECO:0000250}.

Recessive Scores

• pRec: 0.130

Intolerance Scores

• rvis_EVS: -0.08
• rvis_percentile_EVS: 47.79

Haploinsufficiency Scores

• pHI: 0.511
• hipred: Y
• hipred_score: 0.736
• ghis: 0.478

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.704

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sox14

Zebrafish Information Network

• Gene name: sox14
• Affected structure: hypothalamus development
• Phenotype tag: abnormal
• Phenotype quality: disrupted

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;regulation of transcription, DNA-templated;nervous system development;visual perception;entrainment of circadian clock;cell differentiation;negative regulation of transcription, DNA-templated;regulation of neuron migration
• Cellular component: cellular_component;nucleus;nuclear transcription factor complex
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;chromatin binding;protein binding;sequence-specific DNA binding;protein heterodimerization activity