DNPEP

aspartyl aminopeptidase, the group of Aminopeptidases

Basic information

Region (hg38): 2:219372029-219400022

Links

ENSG00000123992 ∙ NCBI:23549 ∙ OMIM:611367 ∙ HGNC:2981 ∙ Uniprot:Q9ULA0 ∙ 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 DNPEP gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DNPEP 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			39	1	1	41
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	39	1	1

Variants in DNPEP

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

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

Position	Type	Phenotype	Significance	ClinVar
2-219374335-A-G		not specified	Uncertain significance (Jun 05, 2024)
2-219374881-C-T		not specified	Uncertain significance (Dec 16, 2023)
2-219374949-C-T		not specified	Uncertain significance (Oct 10, 2023)
2-219374961-C-T		not specified	Uncertain significance (Dec 20, 2023)
2-219374976-G-A		not specified	Uncertain significance (Dec 08, 2023)
2-219381369-C-T		not specified	Uncertain significance (Aug 11, 2024)
2-219381405-C-T		not specified	Uncertain significance (Mar 07, 2023)
2-219381406-G-A		not specified	Uncertain significance (Dec 05, 2024)
2-219381413-G-C		not specified	Uncertain significance (Jun 24, 2022)
2-219381562-G-A		not specified	Uncertain significance (Jan 22, 2024)
2-219381995-C-T		not specified	Uncertain significance (Mar 16, 2022)
2-219382054-G-A		not specified	Uncertain significance (Sep 17, 2021)
2-219382081-C-A		not specified	Uncertain significance (May 02, 2024)
2-219382115-C-A		not specified	Uncertain significance (Apr 26, 2024)
2-219382135-C-A		not specified	Uncertain significance (Aug 17, 2021)
2-219382145-G-A			Benign (May 09, 2018)
2-219383136-C-T		not specified	Uncertain significance (Dec 13, 2021)
2-219383144-T-C		not specified	Uncertain significance (Mar 07, 2023)
2-219383160-G-A		not specified	Uncertain significance (Oct 10, 2023)
2-219384394-T-C		not specified	Uncertain significance (Dec 07, 2021)
2-219384404-G-A		not specified	Uncertain significance (Sep 09, 2024)
2-219384425-C-T		not specified	Uncertain significance (Jan 02, 2024)
2-219384431-C-A		not specified	Uncertain significance (Oct 01, 2024)
2-219384438-C-G		not specified	Uncertain significance (Dec 10, 2024)
2-219385464-A-G		not specified	Uncertain significance (Mar 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DNPEP	protein_coding	protein_coding	ENST00000273075	15	26477

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.16e-8	0.927	124750	0	63	124813	0.000252

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.367	288	306	0.941	0.0000187	3140
Missense in Polyphen		109	133.76	0.81487		1310
Synonymous	0.803	103	114	0.904	0.00000651	990
Loss of Function	1.84	16	26.1	0.612	0.00000129	294

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000725	0.000716
Ashkenazi Jewish	0.00	0.00
East Asian	0.000504	0.000501
Finnish	0.00	0.00
European (Non-Finnish)	0.000251	0.000247
Middle Eastern	0.000504	0.000501
South Asian	0.000164	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Aminopeptidase with specificity towards an acidic amino acid at the N-terminus. Likely to play an important role in intracellular protein and peptide metabolism. {ECO:0000269|PubMed:9632644}.

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.315
• rvis_EVS: 0.24
• rvis_percentile_EVS: 69.37

Haploinsufficiency Scores

• pHI: 0.359
• hipred: N
• hipred_score: 0.441
• ghis: 0.500

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.397

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dnpep

Gene ontology

• Biological process: proteolysis;peptide metabolic process
• Cellular component: extracellular region;nucleus;cytoplasm;cytosol;blood microparticle
• Molecular function: aminopeptidase activity;protein binding;zinc ion binding;identical protein binding;metalloaminopeptidase activity