PGPEP1L

pyroglutamyl-peptidase I like

Basic information

Region (hg38): 15:98968229-99007792

Links

ENSG00000183571 ∙ NCBI:145814 ∙ ∙ HGNC:27080 ∙ Uniprot:A6NFU8 ∙ 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 PGPEP1L gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PGPEP1L 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			21	2		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	23	2	0

Variants in PGPEP1L

This is a list of pathogenic ClinVar variants found in the PGPEP1L region.

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

Position	Type	Phenotype	Significance	ClinVar
15-98968502-C-T		not specified	Uncertain significance (Dec 07, 2024)
15-98968506-G-A		not specified	Uncertain significance (Aug 19, 2021)
15-98968519-C-T		not specified	Likely benign (Dec 09, 2023)
15-98968557-A-T		not specified	Uncertain significance (Feb 27, 2024)
15-98968558-G-C		not specified	Uncertain significance (Feb 27, 2024)
15-98968560-A-T		not specified	Uncertain significance (Feb 27, 2024)
15-98968573-T-C		not specified	Uncertain significance (Aug 26, 2024)
15-98968597-G-T		not specified	Uncertain significance (Sep 14, 2023)
15-98968602-G-A		not specified	Uncertain significance (Feb 28, 2023)
15-98968615-G-A		not specified	Uncertain significance (May 07, 2024)
15-98968623-G-A		not specified	Uncertain significance (Jan 03, 2024)
15-98968638-A-T		not specified	Uncertain significance (Nov 17, 2022)
15-98968651-C-T		not specified	Uncertain significance (Oct 26, 2022)
15-98968693-C-T		not specified	Uncertain significance (Dec 27, 2023)
15-98969432-C-T		not specified	Uncertain significance (Aug 12, 2024)
15-98969437-C-T		not specified	Uncertain significance (Aug 11, 2022)
15-98969440-G-C		not specified	Uncertain significance (Mar 26, 2024)
15-98969458-C-G		not specified	Uncertain significance (Apr 12, 2023)
15-98969468-C-T		not specified	Uncertain significance (Oct 12, 2022)
15-98969490-C-T		not specified	Uncertain significance (May 14, 2024)
15-98969491-A-G		not specified	Uncertain significance (Nov 21, 2024)
15-98969533-C-T		not specified	Uncertain significance (Jul 26, 2024)
15-98969549-G-T		not specified	Uncertain significance (May 14, 2024)
15-98969551-C-A		not specified	Uncertain significance (Mar 07, 2024)
15-98969560-C-T		not specified	Uncertain significance (Apr 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PGPEP1L	protein_coding	protein_coding	ENST00000378919	4	39566

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.71e-9	0.0245	124827	0	38	124865	0.000152

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.09	154	120	1.28	0.00000834	1227
Missense in Polyphen		42	35.031	1.1989		421
Synonymous	-1.65	71	55.4	1.28	0.00000437	412
Loss of Function	-1.54	10	5.94	1.68	2.54e-7	70

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000293	0.0000293
Ashkenazi Jewish	0.00	0.00
East Asian	0.000167	0.000167
Finnish	0.000606	0.000603
European (Non-Finnish)	0.000125	0.000124
Middle Eastern	0.000167	0.000167
South Asian	0.000131	0.000131
Other	0.000496	0.000494

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.826
• rvis_EVS: 1.28
• rvis_percentile_EVS: 93.77

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.123
• ghis: 0.472

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	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Pgpep1l

Gene ontology

• Biological process: proteolysis
• Molecular function: cysteine-type peptidase activity