DPEP3

dipeptidase 3, the group of M19 metallopeptidases

Basic information

Region (hg38): 16:67975663-67980549

Links

ENSG00000141096 ∙ NCBI:64180 ∙ OMIM:609926 ∙ HGNC:23029 ∙ Uniprot:Q9H4B8 ∙ 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 DPEP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DPEP3 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	2		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	26	2	1

Variants in DPEP3

This is a list of pathogenic ClinVar variants found in the DPEP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-67975859-C-T		not specified	Likely benign (Apr 07, 2022)
16-67975862-T-C		not specified	Likely benign (Jun 02, 2023)
16-67975917-C-T		not specified	Uncertain significance (Aug 02, 2023)
16-67975961-T-A		not specified	Uncertain significance (Aug 09, 2021)
16-67976141-T-G		not specified	Uncertain significance (Jun 13, 2022)
16-67976166-C-T		not specified	Uncertain significance (Jun 07, 2023)
16-67976167-G-A		not specified	Uncertain significance (Nov 18, 2022)
16-67977296-A-G		not specified	Uncertain significance (Jun 24, 2022)
16-67977312-C-A		not specified	Uncertain significance (Nov 10, 2024)
16-67977336-C-T		not specified	Uncertain significance (Sep 26, 2022)
16-67977338-A-T		not specified	Uncertain significance (Oct 12, 2021)
16-67977349-C-A		not specified	Uncertain significance (Aug 02, 2022)
16-67977735-G-C		not specified	Uncertain significance (Sep 27, 2021)
16-67977771-T-C		not specified	Uncertain significance (Aug 10, 2021)
16-67977799-T-C		not specified	Uncertain significance (Oct 12, 2024)
16-67977943-C-G		not specified	Uncertain significance (Mar 23, 2022)
16-67977958-C-T		not specified	Uncertain significance (Jan 23, 2023)
16-67977982-G-A		not specified	Uncertain significance (Mar 24, 2023)
16-67978268-A-G		not specified	Uncertain significance (Sep 27, 2022)
16-67978318-T-A		not specified	Uncertain significance (Oct 06, 2024)
16-67978327-C-T		not specified	Uncertain significance (Oct 01, 2024)
16-67978376-T-G		not specified	Uncertain significance (Aug 20, 2024)
16-67978378-A-G		not specified	Uncertain significance (Jan 16, 2024)
16-67978545-G-A		not specified	Uncertain significance (Dec 20, 2022)
16-67978554-G-A		not specified	Uncertain significance (May 13, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DPEP3	protein_coding	protein_coding	ENST00000268793	10	5167

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.27e-10	0.219	125699	0	47	125746	0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.01	263	314	0.839	0.0000201	3247
Missense in Polyphen		87	102	0.85291		1142
Synonymous	0.268	134	138	0.971	0.00000902	1133
Loss of Function	0.646	16	19.0	0.840	9.52e-7	211

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000362	0.000362
Ashkenazi Jewish	0.00	0.00
East Asian	0.000652	0.000653
Finnish	0.00	0.00
European (Non-Finnish)	0.000132	0.000132
Middle Eastern	0.000652	0.000653
South Asian	0.000393	0.000392
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable metalloprotease which hydrolyzes cystinyl-bis- glycine. May be involved in meiosis (By similarity). {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;Aflatoxin activation and detoxification (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.608
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.61

Haploinsufficiency Scores

• pHI: 0.0501
• hipred: N
• hipred_score: 0.172
• ghis: 0.422

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.543

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dpep3

Gene ontology

• Biological process: proteolysis;male meiotic nuclear division
• Cellular component: acrosomal vesicle;plasma membrane;anchored component of membrane
• Molecular function: metalloexopeptidase activity;dipeptidyl-peptidase activity;dipeptidase activity;metal ion binding