PGPEP1L

protein-coding

pyroglutamyl-peptidase I like

Gene summary

Predicted to enable peptidase activity. Predicted to be involved in proteolysis. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001167902.2

Inheritance

—

ClinVar variants

U:43B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.68

Max pathogenic AF

—

Genomic locus

chr15:98,968,229-99,007,792

External References & Databases

Ensembl (ENSG00000183571)

Transcript & Mutation Effects

hg38 • Region Span ~39.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PGPEP1L variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 45

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001167902.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			42 clinvar	2 clinvar		44
nonsense						0
start loss			1 clinvar			1
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	43	2	0	45

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 26 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001167902.2	RefSeq	NP_001161374.1	2	MANE Select
ENST00000535714.2	Ensembl	ENSP00000437560.1	2	MANE Select
NM_001102612.2	RefSeq	NP_001096082.2	4	Standard
ENST00000378919.6	Ensembl	ENSP00000368199.6	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

proteolysis

Molecular Function

cysteine-type peptidase activity

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000378919
Coding exons: 4
Length: 39566
Individuals with no LoFs: 124827
Homozygous LoFs: 0
Heterozygous LoFs: 38
Defined: 124865
p: 0.000152

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.09	154	120	1.28	0.00000834	1227
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00017	0.00017	rare
Finnish	0.00061	0.00060	rare
European (Non-Finnish)	0.00012	0.00012	rare
South Asian	0.00013	0.00013	rare
Other	0.00050	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.826
RVIS EVS: 1.28
RVIS percentile EVS: 93.77

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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