CATSPER3

protein-coding

cation channel sperm associated 3, the group of Cation channels sperm associated

Gene summary

Predicted to enable voltage-gated calcium channel activity. Predicted to be involved in flagellated sperm motility; sodium ion transport; and sperm capacitation. Located in sperm midpiece and sperm principal piece. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_178019.3

Inheritance

—

ClinVar variants

U:53B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.56

Max pathogenic AF

—

Genomic locus

chr5:134,967,907-135,011,696

External References & Databases

Ensembl (ENSG00000152705)

Transcript & Mutation Effects

hg38 • Region Span ~43.8 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 CATSPER3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 58

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_178019.3. 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			52 clinvar	6 clinvar		58
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	53	8	1	62

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_178019.3	RefSeq	NP_821138.1	8	MANE Select
ENST00000282611.8	Ensembl	ENSP00000282611.6	8	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Fertilization
Reproduction
Sperm Motility And Taxes

Biological Process

sodium ion transport
multicellular organism development
flagellated sperm motility
regulation of ion transmembrane transport
sperm-egg recognition

Molecular Function

voltage-gated calcium channel activity

Cellular Component

acrosomal vesicle
endoplasmic reticulum
plasma membrane
motile cilium
CatSper complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000282611
Coding exons: 8
Length: 43797
Individuals with no LoFs: 125705
Homozygous LoFs: 0
Heterozygous LoFs: 43
Defined: 125748
p: 0.000171

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.328	235	221	1.06	0.0000134	2671
Missense (PolyPhen)		65	65.948	0.98563		846
Synonymous	0.859	74	84.0	0.881	0.00000513	726
Loss of Function	1.63	9	16.1	0.561	7.89e-7	193

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00018	0.00018	rare
Latino/Admixed American	0.00014	0.00014	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00011	0.00011	rare
Finnish	0.00038	0.00037	rare
European (Non-Finnish)	0.00015	0.00015	rare
South Asian	0.00020	0.00020	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Voltage-gated calcium channel that plays a central role in calcium-dependent physiological responses essential for successful fertilization, such as sperm hyperactivation, acrosome reaction and chemotaxis towards the oocyte. {ECO:0000269|PubMed:21412338, ECO:0000269|PubMed:21412339}.;

Recessive Scores

pRec: 0.0864

Intolerance Scores

LoFtool: 0.208
RVIS EVS: 0.85
RVIS percentile EVS: 88.42

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0421

Gene Damage Prediction

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