DPP3

dipeptidyl peptidase 3, the group of M49 metallopeptidase family

Basic information

Region (hg38): 11:66480013-66509657

Links

ENSG00000254986 ∙ NCBI:10072 ∙ OMIM:606818 ∙ HGNC:3008 ∙ Uniprot:Q9NY33 ∙ 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 DPP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DPP3 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	4	5
missense			44		4	48
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region					2	2
non coding					1	1
Total	0	0	45	1	9

Variants in DPP3

This is a list of pathogenic ClinVar variants found in the DPP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-66482219-A-C		not specified	Uncertain significance (Mar 11, 2024)
11-66482229-A-G		not specified	Uncertain significance (Apr 14, 2022)
11-66482234-A-G		not specified	Uncertain significance (Dec 18, 2023)
11-66482247-G-A		not specified	Uncertain significance (Nov 13, 2023)
11-66482259-G-A		not specified	Uncertain significance (Sep 30, 2021)
11-66482265-C-G		not specified	Uncertain significance (May 04, 2022)
11-66482270-C-T		not specified	Uncertain significance (Sep 12, 2023)
11-66482316-G-A		not specified	Uncertain significance (Dec 14, 2021)
11-66482367-C-T		not specified	Uncertain significance (Oct 20, 2023)
11-66482369-C-T		not specified	Uncertain significance (Jun 03, 2024)
11-66482375-A-C		not specified	Uncertain significance (Jun 13, 2024)
11-66482417-G-A		not specified	Uncertain significance (Apr 20, 2023)
11-66482426-C-T		not specified	Uncertain significance (May 07, 2024)
11-66482427-G-A			Benign (Jul 13, 2018)
11-66482456-G-A		not specified	Uncertain significance (Dec 20, 2023)
11-66485168-C-A			Benign (May 21, 2018)
11-66485168-C-G			Benign (May 08, 2018)
11-66485174-C-T		not specified	Uncertain significance (Nov 18, 2022)
11-66485225-C-A		not specified	Uncertain significance (Oct 05, 2023)
11-66486621-G-A		not specified	Uncertain significance (Feb 17, 2022)
11-66486657-C-T		not specified	Uncertain significance (Nov 21, 2022)
11-66486666-C-A			Benign (Jul 13, 2018)
11-66486686-C-G			Benign (Jul 13, 2018)
11-66487343-G-A			Uncertain significance (Jun 02, 2017)
11-66487953-G-A		not specified	Uncertain significance (Sep 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DPP3	protein_coding	protein_coding	ENST00000360510	17	29647

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.80e-11	0.992	125645	0	103	125748	0.000410

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.29	387	465	0.832	0.0000306	4738
Missense in Polyphen		97	135.25	0.7172		1456
Synonymous	0.620	189	200	0.944	0.0000134	1519
Loss of Function	2.54	23	40.4	0.569	0.00000204	435

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00137	0.00134
Ashkenazi Jewish	0.000400	0.000397
East Asian	0.000384	0.000381
Finnish	0.0000467	0.0000462
European (Non-Finnish)	0.000353	0.000343
Middle Eastern	0.000384	0.000381
South Asian	0.000556	0.000555
Other	0.000514	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cleaves and degrades bioactive peptides, including angiotensin, Leu-enkephalin and Met-enkephalin (PubMed:3233187, PubMed:1515063). Also cleaves Arg-Arg-beta-naphthylamide (in vitro) (PubMed:9425109, PubMed:3233187, PubMed:11209758). {ECO:0000269|PubMed:11209758, ECO:0000269|PubMed:1515063, ECO:0000269|PubMed:3233187, ECO:0000269|PubMed:9425109}.

Recessive Scores

• pRec: 0.300

Intolerance Scores

• loftool: 0.868
• rvis_EVS: 0.87
• rvis_percentile_EVS: 88.89

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.199
• ghis: 0.524

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.781

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dpp3

Gene ontology

• Biological process: proteolysis
• Cellular component: cytosol;plasma membrane;nuclear speck;extracellular exosome
• Molecular function: protein binding;metallopeptidase activity;dipeptidyl-peptidase activity;zinc ion binding