SPATA31A6

protein-coding

SPATA31 subfamily A member 6

Gene summary

Predicted to enable actin binding activity. Predicted to be involved in cell differentiation and spermatogenesis. Predicted to be located in acrosomal vesicle. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

FAM75A6

MANE transcript

NM_001145196.1

Inheritance

—

ClinVar variants

U:338B:47

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.4

Max pathogenic AF

—

Genomic locus

chr9:42,183,659-42,189,887

External References & Databases

Ensembl (ENSG00000185775)

Transcript & Mutation Effects

hg38 • Region Span ~6.2 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 SPATA31A6 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 376

not providedTotal: 13

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001145196.1. 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				5 clinvar		5
missense			338 clinvar	41 clinvar		379
nonsense				1 clinvar		1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	338	47	0	385

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 3 of 3 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001145196.1	RefSeq	NP_001138668.1	4	MANE Select
ENST00000332857.7	Ensembl	ENSP00000329825.6	4	MANE Select
XM_011517871.4	RefSeq	XP_011516173.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

spermatogenesis
cell differentiation

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000332857
Coding exons: 4
Length: 6224
Individuals with no LoFs: 118846
Homozygous LoFs: 7
Heterozygous LoFs: 13
Defined: 118866
p: 0.0000841

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-4.59	637	384	1.66	0.0000195	8446
Missense (PolyPhen)		134	79.196	1.692		1995
Synonymous	-5.99	248	154	1.61	0.00000814	2666
Loss of Function	-0.771	6	4.28	1.40	1.78e-7	67

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00023	0.00014	rare
Latino/Admixed American	0.00031	0.00021	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00013	0.00010	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May play a role in spermatogenesis. {ECO:0000250}.;

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High