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.

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.

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			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	0	0

Variants in PGPEP1

This is a list of pathogenic ClinVar variants found in the PGPEP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-18340701-C-A		not specified	Uncertain significance (Sep 14, 2022)
19-18342891-G-A		not specified	Uncertain significance (Aug 16, 2021)
19-18355925-G-A		not specified	Uncertain significance (Jun 27, 2022)
19-18357401-G-C		not specified	Uncertain significance (Apr 18, 2023)
19-18357408-G-C		not specified	Uncertain significance (May 16, 2023)
19-18357449-A-C		not specified	Uncertain significance (Jul 26, 2022)
19-18357476-C-T		not specified	Uncertain significance (Aug 30, 2021)
19-18357503-G-A		not specified	Uncertain significance (Sep 17, 2021)
19-18357528-A-G		not specified	Uncertain significance (Jun 28, 2022)
19-18357584-G-A		not specified	Uncertain significance (Jan 25, 2023)
19-18357588-C-T		not specified	Uncertain significance (Sep 21, 2023)
19-18357612-G-A		Malignant tumor of prostate	Uncertain significance (-)
19-18363434-C-T		not specified	Uncertain significance (May 23, 2023)
19-18363560-A-G		not specified	Uncertain significance (Sep 25, 2023)

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