PATE4

protein-coding

prostate and testis expressed 4, the group of LY6/PLAUR domain containing|PATE family

Gene summary

Enables acetylcholine receptor regulator activity. Involved in regulation of neurotransmitter receptor activity. Located in acrosomal vesicle and obsolete extracellular space. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001144874.1

Inheritance

—

ClinVar variants

U:13

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.05

Max pathogenic AF

—

Genomic locus

chr11:125,833,316-125,840,072

External References & Databases

Ensembl (ENSG00000237353)

Transcript & Mutation Effects

hg38 • Region Span ~6.8 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 PATE4 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 12

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001144874.1. 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			12 clinvar			12
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	13	0	0	13

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 4 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001144874.1	RefSeq	NP_001138346.1	3	MANE Select
ENST00000457514.3	Ensembl	ENSP00000411439.2	3	MANE Select
ENST00000534411.5	Ensembl	ENSP00000435472.1	2	Standard
ENST00000534411.6	Ensembl	ENSP00000435472.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of neurotransmitter receptor activity

Molecular Function

acetylcholine receptor regulator activity

Cellular Component

acrosomal vesicle
extracellular space

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000457514
Coding exons: 3
Length: 6754
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	0.176	43	46.4	0.927	0.00000219	632
Missense (PolyPhen)		10	9.6038	1.0413		128
Synonymous	0.249	15	16.3	0.921	7.02e-7	170
Loss of Function	-0.0886	4	3.81	1.05	2.47e-7	41

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: May modulate the function of nicotinic acetylcholine receptors. May enhance sperm motility. {ECO:0000269|PubMed:18387948}.;

Intolerance Scores

RVIS EVS: 0.83
RVIS percentile EVS: 88.16

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	High	Medium	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High