PATE2

protein-coding

prostate and testis expressed 2, the group of LY6/PLAUR domain containing|PATE family

Gene summary

Located in obsolete extracellular space. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C11orf38

MANE transcript

NM_212555.3

Inheritance

—

ClinVar variants

U:24

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.91

Max pathogenic AF

—

Genomic locus

chr11:125,776,113-125,778,828

External References & Databases

Ensembl (ENSG00000196844)

Transcript & Mutation Effects

hg38 • Region Span ~2.7 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 PATE2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 23

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_212555.3. 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			23 clinvar			23
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	24	0	0	24

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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_212555.3	RefSeq	NP_997720.1	4	MANE Select
ENST00000358524.8	Ensembl	ENSP00000351325.3	4	MANE Select
ENST00000436890.2	Ensembl	ENSP00000414895.2	3	Standard
ENST00000436890.3	Ensembl	ENSP00000414895.2	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

extracellular space

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000358524
Coding exons: 4
Length: 2707
Individuals with no LoFs: 125653
Homozygous LoFs: 0
Heterozygous LoFs: 33
Defined: 125686
p: 0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.295	66	59.6	1.11	0.00000267	748
Missense (PolyPhen)		19	21.627	0.87854		266
Synonymous	-0.650	26	22.1	1.18	0.00000109	194
Loss of Function	0.202	5	5.51	0.907	2.31e-7	73

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00049	0.00049	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00017	0.00017	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.542
RVIS EVS: -0.12
RVIS percentile EVS: 44.54

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.311

Gene Damage Prediction

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