XPNPEP1

X-prolyl aminopeptidase 1, the group of Aminopeptidases|M24 metallopeptidase family

Basic information

Region (hg38): 10:109864766-109923553

Previous symbols: [ "XPNPEP", "XPNPEPL1", "XPNPEPL" ]

Links

ENSG00000108039 ∙ NCBI:7511 ∙ OMIM:602443 ∙ HGNC:12822 ∙ Uniprot:Q9NQW7 ∙ 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 XPNPEP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the XPNPEP1 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			24	1		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	2	0

Variants in XPNPEP1

This is a list of pathogenic ClinVar variants found in the XPNPEP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-109865219-T-G		not specified	Uncertain significance (May 31, 2022)
10-109865253-C-A		not specified	Uncertain significance (Dec 06, 2022)
10-109865261-C-T		not specified	Uncertain significance (Dec 01, 2022)
10-109865269-A-G		not specified	Uncertain significance (Feb 02, 2024)
10-109865273-C-T		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
10-109865289-G-T		not specified	Uncertain significance (Nov 09, 2021)
10-109868641-T-C		not specified	Uncertain significance (Mar 14, 2024)
10-109868696-C-T		not specified	Uncertain significance (Mar 07, 2024)
10-109869991-T-C		not specified	Uncertain significance (Mar 24, 2023)
10-109870866-C-T		not specified	Uncertain significance (May 02, 2024)
10-109871813-C-T		not specified	Likely benign (Mar 21, 2023)
10-109873399-T-C		not specified	Uncertain significance (Dec 20, 2023)
10-109873400-T-C			Likely benign (Nov 01, 2022)
10-109875549-A-G		not specified	Uncertain significance (Aug 08, 2023)
10-109875594-A-C		not specified	Uncertain significance (May 24, 2024)
10-109875597-G-T		not specified	Uncertain significance (May 24, 2023)
10-109880849-C-T		not specified	Uncertain significance (Feb 27, 2024)
10-109880916-T-C		not specified	Uncertain significance (Aug 15, 2023)
10-109882624-G-T		not specified	Uncertain significance (Jul 25, 2023)
10-109884082-C-G		not specified	Uncertain significance (Feb 02, 2024)
10-109884085-A-G		not specified	Uncertain significance (May 08, 2024)
10-109886281-A-G		not specified	Uncertain significance (Apr 22, 2022)
10-109886314-T-G		not specified	Uncertain significance (Jan 29, 2024)
10-109888154-C-T		not specified	Uncertain significance (Jan 09, 2024)
10-109888556-C-T		not specified	Uncertain significance (Oct 29, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
XPNPEP1	protein_coding	protein_coding	ENST00000502935	21	58788

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.333	0.667	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.42	253	387	0.653	0.0000219	4369
Missense in Polyphen		53	127.17	0.41677		1376
Synonymous	-1.18	158	140	1.13	0.00000829	1273
Loss of Function	4.49	9	39.4	0.229	0.00000195	466

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.0000617	0.0000615
Middle Eastern	0.000272	0.000272
South Asian	0.0000655	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Contributes to the degradation of bradykinin. Catalyzes the removal of a penultimate prolyl residue from the N-termini of peptides, such as Arg-Pro-Pro.

Recessive Scores

• pRec: 0.278

Intolerance Scores

• loftool: 0.0818
• rvis_EVS: -0.73
• rvis_percentile_EVS: 14.02

Haploinsufficiency Scores

• pHI: 0.188
• hipred: Y
• hipred_score: 0.625
• ghis: 0.635

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.881

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Xpnpep1
• Phenotype: homeostasis/metabolism phenotype; craniofacial phenotype; muscle phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; respiratory system phenotype; embryo phenotype; skeleton phenotype; renal/urinary system phenotype; immune system phenotype; vision/eye phenotype; digestive/alimentary 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); neoplasm; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); liver/biliary system phenotype

Gene ontology

• Biological process: proteolysis;bradykinin catabolic process
• Cellular component: cytoplasm;cytosol;extracellular exosome
• Molecular function: aminopeptidase activity;manganese ion binding;protein homodimerization activity;metalloaminopeptidase activity