DPEP2

dipeptidase 2, the group of M19 metallopeptidases

Basic information

Region (hg38): 16:67987394-68000586

Links

ENSG00000167261 ∙ NCBI:64174 ∙ OMIM:609925 ∙ HGNC:23028 ∙ Uniprot:Q9H4A9 ∙ 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 DPEP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DPEP2 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			29	2		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	3	0

Variants in DPEP2

This is a list of pathogenic ClinVar variants found in the DPEP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-67987561-A-G		not specified	Uncertain significance (Jan 04, 2024)
16-67987571-A-G		not specified	Uncertain significance (Mar 20, 2023)
16-67987667-G-A		not specified	Uncertain significance (Aug 05, 2024)
16-67987669-A-G		not specified	Uncertain significance (Dec 27, 2023)
16-67987672-C-T		not specified	Likely benign (Aug 02, 2023)
16-67987675-G-A		not specified	Uncertain significance (Mar 01, 2024)
16-67987682-C-T		not specified	Uncertain significance (Feb 28, 2023)
16-67987714-G-A		not specified	Uncertain significance (Jan 30, 2024)
16-67987874-C-T		not specified	Uncertain significance (Aug 17, 2022)
16-67987896-C-T		not specified	Uncertain significance (Jan 04, 2022)
16-67987900-C-G		not specified	Uncertain significance (Jul 15, 2024)
16-67987909-T-G		not specified	Uncertain significance (Oct 20, 2023)
16-67990082-T-G		not specified	Uncertain significance (Nov 30, 2022)
16-67990838-C-A		not specified	Uncertain significance (Oct 12, 2022)
16-67990874-G-A		not specified	Uncertain significance (Nov 14, 2024)
16-67990882-G-A		not specified	Uncertain significance (Jul 14, 2023)
16-67990897-A-T		not specified	Uncertain significance (Apr 07, 2022)
16-67990904-C-T		not specified	Uncertain significance (Jun 30, 2022)
16-67990913-C-T		not specified	Uncertain significance (Sep 22, 2023)
16-67990916-C-T		not specified	Uncertain significance (Dec 13, 2022)
16-67990927-C-T		not specified	Uncertain significance (Nov 30, 2022)
16-67990928-G-A		not specified	Uncertain significance (Jun 05, 2023)
16-67990961-C-T		not specified	Uncertain significance (Aug 05, 2024)
16-67990963-A-G		not specified	Uncertain significance (Aug 27, 2024)
16-67991135-C-T		not specified	Uncertain significance (Feb 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DPEP2	protein_coding	protein_coding	ENST00000412757	10	13193

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.22e-10	0.168	125237	1	510	125748	0.00203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.331	277	293	0.946	0.0000183	3090
Missense in Polyphen		95	109.33	0.8689		1179
Synonymous	1.31	106	125	0.851	0.00000788	1031
Loss of Function	0.525	16	18.4	0.868	7.84e-7	212

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00162	0.00162
Ashkenazi Jewish	0.00	0.00
East Asian	0.000653	0.000653
Finnish	0.00143	0.00143
European (Non-Finnish)	0.00343	0.00340
Middle Eastern	0.000653	0.000653
South Asian	0.000686	0.000686
Other	0.00244	0.00245

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable metalloprotease which hydrolyzes leukotriene D4 (LTD4) into leukotriene E4 (LTE4). {ECO:0000250}.
• Pathway: Busulfan Pathway, Pharmacodynamics;Metabolism of lipids;Synthesis of Leukotrienes (LT) and Eoxins (EX);Arachidonic acid metabolism;Biological oxidations;Metabolism;Fatty acid metabolism;leukotriene biosynthesis;Aflatoxin activation and detoxification (Consensus)

Recessive Scores

• pRec: 0.115

Intolerance Scores

• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.45

Haploinsufficiency Scores

• pHI: 0.103
• hipred: N
• hipred_score: 0.112
• ghis: 0.516

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.137

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dpep2

Zebrafish Information Network

• Gene name: dpep2
• Affected structure: trunk
• Phenotype tag: abnormal
• Phenotype quality: curved ventral

Gene ontology

• Biological process: proteolysis
• Cellular component: anchored component of membrane
• Molecular function: metalloexopeptidase activity;dipeptidyl-peptidase activity;dipeptidase activity;metal ion binding