PATE1

prostate and testis expressed 1, the group of PATE family|LY6/PLAUR domain containing

Basic information

Region (hg38): 11:125746279-125749867

Links

ENSG00000171053 ∙ NCBI:160065 ∙ OMIM:606861 ∙ HGNC:24664 ∙ Uniprot:Q8WXA2 ∙ 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 PATE1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PATE1 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		1	10
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	1

Variants in PATE1

This is a list of pathogenic ClinVar variants found in the PATE1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-125746672-T-A		not specified	Uncertain significance (Dec 21, 2023)
11-125747379-A-G		not specified	Uncertain significance (Apr 12, 2024)
11-125747715-A-G			Benign (Jan 18, 2019)
11-125747769-G-A		not specified	Uncertain significance (Dec 07, 2023)
11-125747796-C-T		not specified	Uncertain significance (May 26, 2024)
11-125747800-C-G		not specified	Uncertain significance (May 27, 2022)
11-125747804-G-A		not specified	Uncertain significance (Jun 17, 2024)
11-125748688-C-A		not specified	Uncertain significance (Oct 04, 2024)
11-125748693-G-A		not specified	Uncertain significance (Apr 11, 2023)
11-125748720-A-G		not specified	Uncertain significance (Mar 05, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PATE1	protein_coding	protein_coding	ENST00000305738	5	3575

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.38e-9	0.0222	125646	0	91	125737	0.000362

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.480	75	64.2	1.17	0.00000271	834
Missense in Polyphen		22	19.037	1.1557		258
Synonymous	-0.283	23	21.3	1.08	9.15e-7	214
Loss of Function	-1.64	10	5.76	1.74	2.42e-7	76

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000174	0.000174
Ashkenazi Jewish	0.00	0.00
East Asian	0.000489	0.000490
Finnish	0.00	0.00
European (Non-Finnish)	0.000195	0.000193
Middle Eastern	0.000489	0.000490
South Asian	0.00167	0.00167
Other	0.000491	0.000489

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0478

Intolerance Scores

• loftool: 0.775
• rvis_EVS: 0.66
• rvis_percentile_EVS: 84.27

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.123

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.167

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pate1

Gene ontology

• Biological process: regulation of neurotransmitter receptor activity
• Cellular component: extracellular region
• Molecular function: protein binding;acetylcholine receptor regulator activity