SPACA7

protein-coding

sperm acrosome associated 7

Gene summary

Predicted to act upstream of or within negative regulation of cell adhesion and single fertilization. Located in acrosomal vesicle. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C13orf28

MANE transcript

NM_145248.5

Inheritance

—

ClinVar variants

U:25B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.83

Max pathogenic AF

—

Genomic locus

chr13:112,376,355-112,434,689

External References & Databases

Ensembl (ENSG00000153498)

Transcript & Mutation Effects

hg38 • Region Span ~58.3 kb

Loading mutation effect viewer...

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 SPACA7 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 27

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_145248.5. 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		1
missense			24 clinvar	3 clinvar		27
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	25	4	0	29

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 26 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_145248.5	RefSeq	NP_660291.2	7	MANE Select
ENST00000283550.8	Ensembl	ENSP00000283550.3	7	MANE Select
ENST00000375699.3	Ensembl	ENSP00000364851.3	6	Standard
ENST00000375699.4	Ensembl	ENSP00000364851.3	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

single fertilization

Cellular Component

acrosomal vesicle
extracellular region
acrosomal lumen

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000283550
Coding exons: 7
Length: 58371
Individuals with no LoFs: 125715
Homozygous LoFs: 0
Heterozygous LoFs: 32
Defined: 125747
p: 0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.121	100	103	0.967	0.00000540	1267
Missense (PolyPhen)		22	25.413	0.8657		321
Synonymous	-0.816	46	39.5	1.17	0.00000227	350
Loss of Function	0.530	10	12.0	0.835	6.06e-7	144

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.00065	0.00065	rare
European (Non-Finnish)	0.000080	0.000079	rare
South Asian	0.000033	0.000033	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in fertilization. Seems not to play a direct role in sperm-egg binding or gamete fusion. {ECO:0000250|UniProtKB:Q9D2S4}.;

Intolerance Scores

RVIS EVS: 0.04
RVIS percentile EVS: 57.15

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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