SOX30

protein-coding

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

Gene summary

This gene encodes a member of the SOX (SRY-related HMG-box) family of transcription factors involved in the regulation of embryonic development and in the determination of the cell fate. The encoded protein acts as a transcriptional regulator when present in a complex with other proteins. It can activate p53 transcription to promote tumor cell apoptosis in lung cancer. The protein may be involved in the differentiation of developing male germ cells. Alternative splicing of this gene results in multiple transcript variants. A related pseudogene has been identified on chromosome 5. [provided by RefSeq, Apr 2015]

MANE transcript

NM_178424.2

Inheritance

—

ClinVar variants

P:1U:108B:14

Top phenotype

SOX30-related male infertility

gnomAD constraint

pLI —, LoF o/e 0.07

Max pathogenic AF

—

Genomic locus

chr5:157,625,679-157,671,480

External References & Databases

Ensembl (ENSG00000039600)

Transcript & Mutation Effects

hg38 • Region Span ~45.8 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SOX30 variants in ClinVar

5 Conditions Cataloged

not specifiedTotal: 110

not providedTotal: 8

SOX30-related male infertilityTotal: 2

Male infertilityTotal: 1

See casesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_178424.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	5 clinvar	2 clinvar	8
missense		1 clinvar	105 clinvar	4 clinvar	3 clinvar	113
nonsense						0
start loss			1 clinvar			1
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	1	108	9	5	123

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 13 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_178424.2	RefSeq	NP_848511.1	5	MANE Select
ENST00000265007.11	Ensembl	ENSP00000265007.6	5	MANE Select
NM_001308165.2	RefSeq	NP_001295094.1	5	Standard
NM_007017.3	RefSeq	NP_008948.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription by RNA polymerase II
spermatogenesis
response to corticosteroid

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific
protein binding
sequence-specific DNA binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000265007
Coding exons: 5
Length: 45802
Individuals with no LoFs: 125734
Homozygous LoFs: 0
Heterozygous LoFs: 13
Defined: 125747
p: 0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.776	378	423	0.894	0.0000237	4781
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00015	0.000088	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.854

Gene Damage Prediction

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