NPEPPS

aminopeptidase puromycin sensitive, the group of Aminopeptidases|M1 metallopeptidases

Basic information

Region (hg38): 17:47522941-47624665

Links

ENSG00000141279 ∙ NCBI:9520 ∙ OMIM:606793 ∙ HGNC:7900 ∙ Uniprot:P55786 ∙ 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 NPEPPS gene.

• Inborn genetic diseases (15 variants)
• not provided (10 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NPEPPS 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	3	4
missense			15	2		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	2	3
non coding				1		1
Total	0	0	15	4	3

Variants in NPEPPS

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

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

Position	Type	Phenotype	Significance	ClinVar
17-47531338-G-T		not specified	Uncertain significance (Dec 14, 2023)
17-47531344-T-C		not specified	Uncertain significance (Sep 14, 2022)
17-47531382-G-C		not specified	Likely benign (Apr 07, 2023)
17-47531385-T-C		not specified	Likely benign (Apr 07, 2023)
17-47531409-C-T		not specified	Uncertain significance (Jul 19, 2022)
17-47531418-C-T			Benign (Jul 26, 2018)
17-47531519-C-T			Likely benign (Dec 31, 2019)
17-47531554-A-G		not specified	Uncertain significance (Dec 16, 2023)
17-47545902-C-T			Likely benign (Mar 01, 2023)
17-47582823-A-G		not specified	Uncertain significance (Nov 13, 2023)
17-47585524-C-T		not specified	Uncertain significance (Oct 06, 2021)
17-47585666-T-C		not specified	Uncertain significance (Aug 06, 2021)
17-47587239-A-G			Benign (Jun 27, 2018)
17-47587320-A-G			Benign (Jul 13, 2018)
17-47587351-AATATTTTTAAGTGCTCAAAT-A			Likely benign (Dec 30, 2023)
17-47590709-G-C			Benign (Jul 13, 2018)
17-47590838-G-A		not specified	Uncertain significance (Dec 09, 2023)
17-47590876-A-G		not specified	Uncertain significance (Nov 27, 2023)
17-47592050-T-C		not specified	Uncertain significance (Aug 12, 2021)
17-47596446-A-G		not specified	Uncertain significance (Oct 12, 2021)
17-47599679-G-A		not specified	Uncertain significance (Dec 26, 2023)
17-47601671-C-G		not specified	Uncertain significance (Dec 15, 2022)
17-47601712-G-A		not specified	Uncertain significance (Aug 15, 2023)
17-47603942-C-T		not specified	Uncertain significance (Jul 14, 2021)
17-47603954-A-T		not specified	Uncertain significance (Mar 04, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NPEPPS	protein_coding	protein_coding	ENST00000322157	23	100335

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	2.89e-8	121529	0	3	121532	0.0000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.98	222	463	0.479	0.0000236	5944
Missense in Polyphen		35	161.24	0.21706		2125
Synonymous	0.893	148	162	0.911	0.00000815	1733
Loss of Function	6.42	0	48.0	0.00	0.00000245	623

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000303	0.0000303
Ashkenazi Jewish	0.00	0.00
East Asian	0.000112	0.000112
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.000112	0.000112
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Aminopeptidase with broad substrate specificity for several peptides. Involved in proteolytic events essential for cell growth and viability. May act as regulator of neuropeptide activity. Plays a role in the antigen-processing pathway for MHC class I molecules. Involved in the N-terminal trimming of cytotoxic T-cell epitope precursors. Digests the poly-Q peptides found in many cellular proteins. Digests tau from normal brain more efficiently than tau from Alzheimer disease brain. {ECO:0000269|PubMed:10978616, ECO:0000269|PubMed:11062501, ECO:0000269|PubMed:17154549, ECO:0000269|PubMed:17318184, ECO:0000269|PubMed:19917696}.

Recessive Scores

• pRec: 0.200

Intolerance Scores

• loftool: 0.374
• rvis_EVS: 0.04
• rvis_percentile_EVS: 57.31

Haploinsufficiency Scores

• pHI: 0.206
• hipred: N
• hipred_score: 0.380
• ghis: 0.481

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.795

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Npepps
• Phenotype: integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; reproductive system phenotype; 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: protein polyubiquitination;proteolysis;peptide catabolic process;cellular response to hypoxia;positive regulation of protein targeting to mitochondrion
• Cellular component: nucleus;cytoplasm;cytosol;extracellular exosome
• Molecular function: aminopeptidase activity;zinc ion binding;peptide binding;metalloaminopeptidase activity