QPCTL

glutaminyl-peptide cyclotransferase like, the group of M28 metallopeptidases

Basic information

Region (hg38): 19:45692403-45703989

Links

ENSG00000011478 ∙ NCBI:54814 ∙ ∙ HGNC:25952 ∙ Uniprot:Q9NXS2 ∙ 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 QPCTL gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the QPCTL 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				1		1
missense			30	1	1	32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	2	1

Variants in QPCTL

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

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

Position	Type	Phenotype	Significance	ClinVar
19-45692731-C-T		not specified	Uncertain significance (Aug 25, 2021)
19-45692741-T-G		not specified	Uncertain significance (Nov 30, 2021)
19-45692828-T-G		not specified	Uncertain significance (Apr 06, 2024)
19-45692852-C-A		not specified	Uncertain significance (Oct 07, 2024)
19-45692866-T-C		not specified	Uncertain significance (Apr 06, 2022)
19-45692885-A-G		not specified	Uncertain significance (Jan 09, 2024)
19-45692909-G-T		not specified	Uncertain significance (Feb 23, 2023)
19-45693413-G-A		not specified	Uncertain significance (Jan 19, 2022)
19-45693425-G-A		not specified	Uncertain significance (Jul 27, 2024)
19-45693525-C-T		not specified	Uncertain significance (Nov 15, 2021)
19-45693530-A-T		not specified	Uncertain significance (Jun 02, 2024)
19-45695471-G-A		not specified	Uncertain significance (Mar 01, 2023)
19-45695494-T-A		not specified	Uncertain significance (Feb 16, 2023)
19-45695522-T-G		not specified	Uncertain significance (Jul 14, 2023)
19-45695536-G-A		not specified	Uncertain significance (Aug 23, 2021)
19-45695567-G-A			Benign (May 08, 2018)
19-45695576-C-A		not specified	Uncertain significance (Oct 28, 2024)
19-45695588-A-G		not specified	Uncertain significance (Jan 26, 2022)
19-45695618-C-T		not specified	Uncertain significance (Dec 06, 2022)
19-45695692-C-G		not specified	Uncertain significance (Sep 15, 2021)
19-45698551-C-G		not specified	Uncertain significance (Apr 04, 2023)
19-45698595-C-A		not specified	Uncertain significance (Jul 27, 2024)
19-45698608-G-A		not specified	Uncertain significance (Nov 13, 2024)
19-45698655-G-A		not specified	Uncertain significance (Mar 29, 2022)
19-45698683-C-T		not specified	Uncertain significance (Jul 12, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
QPCTL	protein_coding	protein_coding	ENST00000012049	7	11507

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.57e-8	0.225	125699	0	49	125748	0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.616	203	229	0.885	0.0000132	2380
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000548	0.000545
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000196	0.000193
Middle Eastern	0.000218	0.000217
South Asian	0.000196	0.000196
Other	0.000166	0.000163

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.254
• hipred: N
• hipred_score: 0.293
• ghis: 0.476

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.625

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Qpctl
• 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: peptidyl-pyroglutamic acid biosynthetic process, using glutaminyl-peptide cyclotransferase
• Cellular component: Golgi membrane;Golgi apparatus;membrane;integral component of membrane
• Molecular function: zinc ion binding;glutaminyl-peptide cyclotransferase activity