SPATA4

protein-coding

spermatogenesis associated 4, the group of Cilia and flagella associated

Gene summary

Predicted to enable microtubule binding activity. Predicted to be involved in regulation of cytoskeleton organization. Located in nucleoplasm. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_144644.4

Inheritance

—

ClinVar variants

P:1U:48B:4

Top phenotype

Primary ciliary dyskinesia

gnomAD constraint

pLI —, LoF o/e 0.97

Max pathogenic AF

—

Genomic locus

chr4:176,184,579-176,195,585

External References & Databases

Ensembl (ENSG00000150628)

Transcript & Mutation Effects

hg38 • Region Span ~11.0 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 SPATA4 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 48

not providedTotal: 1

Primary ciliary dyskinesiaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_144644.4. 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			46 clinvar	3 clinvar		49
nonsense						0
start loss						0
frameshift	1 clinvar					1
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	1	0	48	4	0	53

Highest pathogenic variant AF is 0.0007192836

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 10 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_144644.4	RefSeq	NP_653245.2	6	MANE Select
ENST00000280191.7	Ensembl	ENSP00000280191.2	6	MANE Select
ENST00000508699.1	Ensembl	ENSP00000425950.1	2	Standard
ENST00000515234.1	Ensembl	ENSP00000422290.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

cilium-dependent cell motility

Molecular Function

molecular_function
protein binding

Cellular Component

cellular_component
nucleus
cytoplasm
motile cilium

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000280191
Coding exons: 6
Length: 11034
Individuals with no LoFs: 125132
Homozygous LoFs: 2
Heterozygous LoFs: 614
Defined: 125748
p: 0.00245

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.319	171	160	1.07	0.00000773	1968
Missense (PolyPhen)		46	42.516	1.082		568
Synonymous	1.22	47	58.9	0.798	0.00000276	585
Loss of Function	0.113	14	14.5	0.968	7.76e-7	176

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00081	0.00080	rare
Latino/Admixed American	0.00070	0.00069	rare
Ashkenazi Jewish	0.00050	0.00050	rare
East Asian	0.00017	0.00016	rare
Finnish	0.0056	0.0057	notable
European (Non-Finnish)	0.0033	0.0033	notable
South Asian	0.0021	0.0020	notable
Other	0.0023	0.0023	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May play a role in apoptosis regulation. {ECO:0000269|PubMed:26424010}.;

Recessive Scores

pRec: 0.0609

Intolerance Scores

RVIS EVS: 0.24
RVIS percentile EVS: 69.21

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0392

Gene Damage Prediction

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