PGPEP1

pyroglutamyl-peptidase I

Basic information

Region (hg38): 19:18340598-18369950

Links

ENSG00000130517 ∙ NCBI:54858 ∙ OMIM:610694 ∙ HGNC:13568 ∙ Uniprot:Q9NXJ5 ∙ 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 PGPEP1 gene.

• not_specified (29 variants)
• Prostate_cancer (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PGPEP1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000017712.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			30			30
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	30	0	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PGPEP1	protein_coding	protein_coding	ENST00000269919	5	29364

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00850	0.939	125729	0	18	125747	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.354	116	127	0.912	0.00000750	1341
Missense in Polyphen		27	37.691	0.71635		388
Synonymous	-0.565	67	61.4	1.09	0.00000466	404
Loss of Function	1.68	5	11.0	0.454	6.20e-7	110

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000173	0.000173
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000535	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.000196	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Removes 5-oxoproline from various penultimate amino acid residues except L-proline. {ECO:0000269|PubMed:12651114}.

Recessive Scores

• pRec: 0.219

Intolerance Scores

• loftool: 0.574
• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.58

Haploinsufficiency Scores

• pHI: 0.267
• hipred: N
• hipred_score: 0.389
• ghis: 0.474

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.508

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pgpep1

Gene ontology

• Biological process: proteolysis
• Cellular component: cytosol
• Molecular function: cysteine-type peptidase activity;pyroglutamyl-peptidase activity