NPEPL1

aminopeptidase like 1, the group of Aminopeptidases

Basic information

Region (hg38): 20:58689131-58719238

Links

ENSG00000215440 ∙ NCBI:79716 ∙ ∙ HGNC:16244 ∙ Uniprot:Q8NDH3 ∙ 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 NPEPL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NPEPL1 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			52	1		53
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	52	2	0

Variants in NPEPL1

This is a list of pathogenic ClinVar variants found in the NPEPL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-58691463-G-A			Likely benign (Dec 01, 2022)
20-58692913-G-T		not specified	Uncertain significance (Jun 05, 2024)
20-58692934-G-A		not specified	Uncertain significance (Feb 08, 2022)
20-58692938-G-C		not specified	Uncertain significance (Dec 16, 2024)
20-58692959-G-C		not specified	Uncertain significance (Jun 28, 2022)
20-58692983-T-C		not specified	Uncertain significance (Oct 13, 2023)
20-58693012-C-T		not specified	Uncertain significance (Jul 27, 2021)
20-58693036-C-T		not specified	Uncertain significance (Feb 06, 2024)
20-58693045-G-A		not specified	Uncertain significance (Sep 03, 2024)
20-58693048-G-A		not specified	Uncertain significance (Nov 17, 2023)
20-58693755-A-G		not specified	Uncertain significance (Jul 22, 2022)
20-58693822-T-A		not specified	Uncertain significance (Dec 25, 2024)
20-58693844-C-G		not specified	Uncertain significance (Nov 21, 2023)
20-58693860-G-A		not specified	Uncertain significance (Jul 26, 2021)
20-58693875-C-G		not specified	Uncertain significance (Aug 27, 2024)
20-58693897-C-T		not specified	Uncertain significance (Sep 26, 2024)
20-58693920-G-A		not specified	Uncertain significance (Jan 02, 2024)
20-58693921-T-C		not specified	Uncertain significance (Mar 01, 2023)
20-58694462-C-T		not specified	Uncertain significance (Aug 29, 2024)
20-58694471-G-A		not specified	Uncertain significance (Jul 06, 2022)
20-58694471-G-C		not specified	Uncertain significance (Jan 19, 2025)
20-58694509-C-T		not specified	Uncertain significance (May 30, 2023)
20-58694512-C-T		not specified	Uncertain significance (Mar 19, 2024)
20-58694513-G-A		not specified	Uncertain significance (Nov 21, 2024)
20-58694528-C-T		not specified	Uncertain significance (Oct 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NPEPL1	protein_coding	protein_coding	ENST00000356091	12	30108

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.85e-7	0.788	124991	0	46	125037	0.000184

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.510	265	289	0.916	0.0000189	3286
Missense in Polyphen		74	89.04	0.83108		939
Synonymous	0.213	132	135	0.977	0.00000996	1104
Loss of Function	1.33	12	18.1	0.662	8.44e-7	252

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00132	0.00124
Ashkenazi Jewish	0.00	0.00
East Asian	0.000295	0.000278
Finnish	0.0000478	0.0000464
European (Non-Finnish)	0.0000829	0.0000795
Middle Eastern	0.000295	0.000278
South Asian	0.000176	0.000163
Other	0.000343	0.000328

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probably catalyzes the removal of unsubstituted N- terminal amino acids from various peptides.

Recessive Scores

• pRec: 0.132

Intolerance Scores

• loftool: 0.764
• rvis_EVS: -0.73
• rvis_percentile_EVS: 14.14

Haploinsufficiency Scores

• pHI: 0.136
• hipred: N
• hipred_score: 0.284
• ghis: 0.573

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.249

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Npepl1

Gene ontology

• Biological process: proteolysis
• Cellular component: nucleus;cytoplasm
• Molecular function: aminopeptidase activity;metalloexopeptidase activity;manganese ion binding