PATE2

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

Basic information

Region (hg38): 11:125776112-125778828

Previous symbols: [ "C11orf38" ]

Links

ENSG00000196844 ∙ NCBI:399967 ∙ ∙ HGNC:32249 ∙ Uniprot:Q6UY27 ∙ 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 PATE2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PATE2 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in PATE2

This is a list of pathogenic ClinVar variants found in the PATE2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-125777402-T-G		not specified	Uncertain significance (Jun 16, 2022)
11-125777446-G-A		not specified	Uncertain significance (Mar 02, 2023)
11-125777482-A-C		not specified	Uncertain significance (Nov 28, 2023)
11-125777508-C-G		not specified	Uncertain significance (Dec 02, 2021)
11-125777508-C-T		not specified	Uncertain significance (Sep 14, 2021)
11-125777903-A-C		not specified	Uncertain significance (Mar 14, 2023)
11-125777904-C-A		not specified	Uncertain significance (Jul 08, 2022)
11-125777951-T-C		not specified	Uncertain significance (Nov 14, 2023)
11-125777963-A-C		not specified	Uncertain significance (Aug 04, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PATE2	protein_coding	protein_coding	ENST00000358524	4	2707

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000558	0.483	125653	0	33	125686	0.000131

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.295	66	59.6	1.11	0.00000267	748
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000116	0.000116
Ashkenazi Jewish	0.00	0.00
East Asian	0.000490	0.000489
Finnish	0.00	0.00
European (Non-Finnish)	0.000168	0.000167
Middle Eastern	0.000490	0.000489
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.542
• rvis_EVS: -0.12
• rvis_percentile_EVS: 44.54

Haploinsufficiency Scores

• pHI: 0.136
• hipred: N
• hipred_score: 0.123
• ghis: 0.468

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.311

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pate2
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Gene ontology

• Cellular component: extracellular space