SPACA4

protein-coding

sperm acrosome associated 4, the group of LY6/PLAUR domain containing

Gene summary

Involved in binding activity of sperm to zona pellucida. Located in inner acrosomal membrane and outer acrosomal membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_133498.3

Inheritance

—

ClinVar variants

U:15B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0

Max pathogenic AF

—

Genomic locus

chr19:48,606,742-48,607,714

External References & Databases

Ensembl (ENSG00000177202)

Transcript & Mutation Effects

hg38 • Region Span ~1.0 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 SPACA4 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 18

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_133498.3. 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						0
missense			15 clinvar	3 clinvar		18
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	15	3	0	18

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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_133498.3	RefSeq	NP_598005.1	1	MANE Select
ENST00000321762.3	Ensembl	ENSP00000312774.1	1	MANE Select
ENST00001103849.1	Ensembl	ENSP00000773652.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Post-translational modification: synthesis of GPI-anchored proteins
Post-translational protein modification
Metabolism of proteins

Biological Process

cell adhesion

Cellular Component

acrosomal vesicle
extracellular region
plasma membrane
anchored component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000321762
Coding exons: 1
Length: 971
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.906	57	79.8	0.715	0.00000521	781
Missense (PolyPhen)		17	29.099	0.58421		281
Synonymous	0.958	31	38.6	0.804	0.00000305	269
Loss of Function	0.152	0	0.0268	0.00	9.19e-10	1

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
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	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Sperm surface membrane protein that may be involved in sperm-egg plasma membrane adhesion and fusion during fertilization.;

Recessive Scores

pRec: 0.107

Intolerance Scores

LoFtool: 0.306
RVIS EVS: 0.24
RVIS percentile EVS: 68.98

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.307

Gene Damage Prediction

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