PATE3

prostate and testis expressed 3, the group of PATE family|LY6/PLAUR domain containing

Basic information

Region (hg38): 11:125788127-125791600

Links

ENSG00000236027 ∙ NCBI:100169851 ∙ ∙ HGNC:35426 ∙ Uniprot:B3GLJ2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PATE3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PATE3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	0	0

Variants in PATE3

This is a list of pathogenic ClinVar variants found in the PATE3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-125789386-C-T		not specified	Uncertain significance (Jun 22, 2021)
11-125789427-C-T		not specified	Uncertain significance (Feb 06, 2025)
11-125789436-C-T		not specified	Uncertain significance (Sep 11, 2024)
11-125789439-T-C		not specified	Uncertain significance (May 04, 2023)
11-125789476-G-T		not specified	Uncertain significance (Oct 26, 2021)
11-125789480-G-C		not specified	Uncertain significance (Feb 16, 2023)
11-125790503-G-T		not specified	Uncertain significance (Jan 02, 2024)
11-125790537-G-C		not specified	Uncertain significance (Jun 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PATE3	protein_coding	protein_coding	ENST00000445202	3	3490

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0473	0.695	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.814	37	53.8	0.688	0.00000307	643
Missense in Polyphen		14	19.452	0.71972		233
Synonymous	1.38	10	17.3	0.579	8.27e-7	169
Loss of Function	0.614	2	3.18	0.628	2.22e-7	34

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: 0.35
• rvis_percentile_EVS: 73.79

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pate3

Gene ontology

• Cellular component: extracellular region