QPCTL

protein-coding

glutaminyl-peptide cyclotransferase like, the group of M28 metallopeptidases

Gene summary

Enables glutaminyl-peptide cyclotransferase activity and zinc ion binding activity. Located in Golgi apparatus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_017659.4

Inheritance

—

ClinVar variants

U:78B:4

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.88

Max pathogenic AF

—

Genomic locus

chr19:45,692,403-45,703,989

External References & Databases

Ensembl (ENSG00000011478)

Transcript & Mutation Effects

hg38 • Region Span ~11.6 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 QPCTL variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 74

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017659.4. 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				2 clinvar		2
missense			74 clinvar	1 clinvar	1 clinvar	76
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	78	3	1	82

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 15 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017659.4	RefSeq	NP_060129.2	7	MANE Select
ENST00000012049.10	Ensembl	ENSP00000012049.4	7	MANE Select
NM_001163377.2	RefSeq	NP_001156849.1	6	Standard
ENST00000366382.8	Ensembl	ENSP00000387944.2	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

peptidyl-pyroglutamic acid biosynthetic process, using glutaminyl-peptide cyclotransferase

Molecular Function

zinc ion binding
glutaminyl-peptide cyclotransferase activity

Cellular Component

Golgi membrane
Golgi apparatus
membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000012049
Coding exons: 7
Length: 11507
Individuals with no LoFs: 125699
Homozygous LoFs: 0
Heterozygous LoFs: 49
Defined: 125748
p: 0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.616	203	229	0.885	0.0000132	2380
Missense (PolyPhen)		85	93.625	0.90788		978
Synonymous	-1.03	119	106	1.13	0.00000633	880
Loss of Function	0.435	13	14.8	0.878	6.32e-7	161

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.00024	0.00023	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00020	0.00019	rare
South Asian	0.00020	0.00020	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Responsible for the biosynthesis of pyroglutamyl peptides. {ECO:0000269|PubMed:18486145, ECO:0000269|PubMed:21288892}.;

Recessive Scores

pRec: 0.107

Intolerance Scores

LoFtool: 0.767
RVIS EVS: 0.29
RVIS percentile EVS: 71.5

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.625

Gene Damage Prediction

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