SPATA31D1

protein-coding

SPATA31 subfamily D member 1

Gene summary

Predicted to be involved in cell differentiation and spermatogenesis. Predicted to be located in membrane. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

FAM75D1

MANE transcript

NM_001001670.3

Inheritance

—

ClinVar variants

U:367B:35

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.74

Max pathogenic AF

—

Genomic locus

chr9:81,988,772-81,995,253

External References & Databases

Ensembl (ENSG00000214929)

Transcript & Mutation Effects

hg38 • Region Span ~6.5 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 SPATA31D1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 397

not providedTotal: 8

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001001670.3. 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				2 clinvar	1 clinvar	3
missense			367 clinvar	31 clinvar	1 clinvar	399
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	367	33	2	402

Loading ClinVar variants...

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_001001670.3	RefSeq	NP_001001670.1	4	MANE Select
ENST00000344803.3	Ensembl	ENSP00000341988.2	4	MANE Select
XM_017014710.3	RefSeq	XP_016870199.1	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: ENST00000344803
Coding exons: 4
Length: 6485
Individuals with no LoFs: 120068
Homozygous LoFs: 0
Heterozygous LoFs: 3
Defined: 120071
p: 0.0000125

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-5.27	1227	806	1.52	0.0000430	10242
Missense (PolyPhen)		189	140.96	1.3408		2169
Synonymous	-5.49	443	318	1.39	0.0000173	3208
Loss of Function	0.567	4	5.43	0.737	2.28e-7	70

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000062	0.000059	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0.000036	0.000034	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

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

Intolerance Scores

RVIS EVS: 0.57
RVIS percentile EVS: 81.74

Essentials

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

Gene Damage Prediction

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