QPCT

glutaminyl-peptide cyclotransferase, the group of M28 metallopeptidases

Basic information

Region (hg38): 2:37342827-37373322

Links

ENSG00000115828 ∙ NCBI:25797 ∙ OMIM:607065 ∙ HGNC:9753 ∙ Uniprot:Q16769 ∙ 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 QPCT gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the QPCT 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			28		1	29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	28	0	1

Variants in QPCT

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

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

Position	Type	Phenotype	Significance	ClinVar
2-37344750-C-T		not specified	Uncertain significance (Apr 24, 2024)
2-37344813-G-C		not specified	Uncertain significance (Feb 13, 2024)
2-37344832-C-T		not specified	Uncertain significance (Jul 20, 2022)
2-37344850-A-C		not specified	Uncertain significance (Feb 05, 2024)
2-37352892-T-C		not specified	Uncertain significance (Jan 31, 2024)
2-37359604-C-T		not specified	Uncertain significance (Nov 09, 2021)
2-37359649-A-C		not specified	Uncertain significance (Oct 17, 2023)
2-37359656-A-G		not specified	Uncertain significance (Jan 25, 2023)
2-37359796-G-A		not specified	Uncertain significance (Nov 09, 2021)
2-37359810-G-T		not specified	Uncertain significance (Mar 27, 2023)
2-37359826-C-T		not specified	Uncertain significance (Aug 26, 2022)
2-37359827-G-A		not specified	Uncertain significance (Jul 25, 2023)
2-37367233-C-G		not specified	Uncertain significance (Nov 08, 2022)
2-37367317-A-T		not specified	Uncertain significance (Aug 04, 2021)
2-37367335-G-A		not specified	Uncertain significance (Feb 06, 2024)
2-37367341-T-C		not specified	Uncertain significance (Aug 04, 2023)
2-37367356-C-T		not specified	Uncertain significance (Mar 15, 2024)
2-37367359-C-T		not specified	Uncertain significance (Sep 06, 2022)
2-37367384-A-C		not specified	Uncertain significance (May 25, 2022)
2-37369709-A-G		not specified	Uncertain significance (Nov 30, 2021)
2-37369727-A-G		not specified	Uncertain significance (Oct 29, 2021)
2-37369739-T-G		not specified	Uncertain significance (Dec 22, 2023)
2-37369742-T-A		not specified	Uncertain significance (Aug 04, 2021)
2-37372400-G-C		not specified	Uncertain significance (Feb 03, 2022)
2-37372407-G-A		not specified	Likely benign (May 13, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
QPCT	protein_coding	protein_coding	ENST00000338415	7	28749

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.20e-15	0.00583	125520	0	228	125748	0.000907

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.940	234	197	1.19	0.0000101	2330
Missense in Polyphen		93	81.998	1.1342		993
Synonymous	-0.345	83	79.1	1.05	0.00000423	717
Loss of Function	-0.319	22	20.4	1.08	0.00000120	217

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00181	0.00181
Ashkenazi Jewish	0.00109	0.00109
East Asian	0.000272	0.000272
Finnish	0.000185	0.000185
European (Non-Finnish)	0.00121	0.00121
Middle Eastern	0.000272	0.000272
South Asian	0.000523	0.000523
Other	0.000652	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Responsible for the biosynthesis of pyroglutamyl peptides. Has a bias against acidic and tryptophan residues adjacent to the N-terminal glutaminyl residue and a lack of importance of chain length after the second residue. Also catalyzes N-terminal pyroglutamate formation. In vitro, catalyzes pyroglutamate formation of N-terminally truncated form of APP amyloid-beta peptides [Glu-3]-amyloid-beta. May be involved in the N-terminal pyroglutamate formation of several amyloid-related plaque-forming peptides. {ECO:0000269|PubMed:15063747, ECO:0000269|PubMed:18486145, ECO:0000269|PubMed:21288892}.
• Pathway: Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.267

Intolerance Scores

• loftool: 0.876
• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.6

Haploinsufficiency Scores

• pHI: 0.346
• hipred: N
• hipred_score: 0.187
• ghis: 0.474

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.222

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Qpct
• Phenotype: homeostasis/metabolism phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: cellular protein modification process;peptidyl-pyroglutamic acid biosynthetic process, using glutaminyl-peptide cyclotransferase;neutrophil degranulation
• Cellular component: extracellular region;specific granule lumen;extracellular exosome;tertiary granule lumen;ficolin-1-rich granule lumen
• Molecular function: zinc ion binding;glutaminyl-peptide cyclotransferase activity