SOX30

SRY-box transcription factor 30, the group of SRY-box transcription factors

Basic information

Region (hg38): 5:157625679-157671480

Links

ENSG00000039600 ∙ NCBI:11063 ∙ OMIM:606698 ∙ HGNC:30635 ∙ Uniprot:O94993 ∙ 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 SOX30 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SOX30 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				2	2	4
missense			59	3	3	65
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	59	5	5

Variants in SOX30

This is a list of pathogenic ClinVar variants found in the SOX30 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-157626368-T-A		See cases	Uncertain significance (-)
5-157626397-T-G		not specified	Uncertain significance (Mar 18, 2024)
5-157626454-A-C		not specified	Uncertain significance (Oct 06, 2023)
5-157626494-C-G		not specified	Uncertain significance (Jan 18, 2025)
5-157626498-G-T		not specified	Uncertain significance (Jul 25, 2023)
5-157626528-T-A		not specified	Uncertain significance (Feb 14, 2023)
5-157626572-C-T		not specified	Uncertain significance (Dec 02, 2022)
5-157626590-G-A		not specified	Uncertain significance (Aug 20, 2024)
5-157626639-T-C		not specified	Uncertain significance (Oct 20, 2023)
5-157626667-C-T		not specified	Uncertain significance (Jan 27, 2022)
5-157626677-G-A		not specified	Uncertain significance (Feb 07, 2025)
5-157626685-T-C		not specified	Likely benign (Nov 09, 2024)
5-157626705-G-A		not specified	Uncertain significance (Dec 22, 2023)
5-157626709-G-A		not specified	Likely benign (Sep 10, 2024)
5-157638272-T-C		not specified	Uncertain significance (Jan 26, 2025)
5-157638285-T-C		not specified	Uncertain significance (May 16, 2023)
5-157638326-G-C		not specified	Uncertain significance (Oct 30, 2024)
5-157638327-G-T		not specified	Uncertain significance (Dec 15, 2022)
5-157638399-C-A		not specified	Uncertain significance (Mar 07, 2025)
5-157638420-G-C		not specified	Uncertain significance (Sep 17, 2021)
5-157638422-T-G			Benign (Dec 31, 2019)
5-157638431-G-A			Benign (Dec 31, 2019)
5-157638435-T-A		not specified	Uncertain significance (Feb 09, 2025)
5-157638465-T-C		not specified	Uncertain significance (Jul 14, 2021)
5-157638491-A-G			Benign (Apr 16, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SOX30	protein_coding	protein_coding	ENST00000265007	5	45802

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.998	0.00175	125734	0	13	125747	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.776	378	423	0.894	0.0000237	4781
Missense in Polyphen		81	119.45	0.67808		1469
Synonymous	1.11	166	185	0.896	0.0000116	1609
Loss of Function	4.49	2	27.3	0.0732	0.00000171	292

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000616	0.0000615
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000150	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional activator. Binds to the DNA sequence 5'- ACAAT-3' and shows a preference for guanine residues surrounding this core motif. {ECO:0000269|PubMed:10359848}.

Recessive Scores

• pRec: 0.0959

Intolerance Scores

• loftool: 0.00338
• rvis_EVS: 1.29
• rvis_percentile_EVS: 93.85

Haploinsufficiency Scores

• pHI: 0.270
• hipred: Y
• hipred_score: 0.584

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.854

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sox30
• Phenotype: reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cellular phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;spermatogenesis;response to corticosteroid
• Cellular component: nucleus
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;protein binding;sequence-specific DNA binding