DPP9

dipeptidyl peptidase 9, the group of DASH family

Basic information

Region (hg38): 19:4674341-4724673

Links

ENSG00000142002 ∙ NCBI:91039 ∙ OMIM:608258 ∙ HGNC:18648 ∙ Uniprot:Q86TI2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hatipoglu immunodeficiency syndrome (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Hatipoglu immunodeficiency syndrome	AR	Allergy/Immunology/Infectious	The condition can include susceptibility to infection, and antiinfectious prophylaxis and early and aggressive treatment of infections may be beneficial; HSCT has been described	Allergy/Immunology/Infectious; Craniofacial; Dermatologic; Musculoskeletal; Neurologic	36112693

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DPP9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DPP9 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				2	3	5
missense			59	6	2	67
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	59	8	5

Variants in DPP9

This is a list of pathogenic ClinVar variants found in the DPP9 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-4679870-G-A		Hatipoglu immunodeficiency syndrome	Pathogenic (Apr 25, 2023)
19-4679927-G-A		not specified	Uncertain significance (Feb 16, 2023)
19-4682745-C-T		not specified	Uncertain significance (May 01, 2022)
19-4682766-C-T		not specified	Uncertain significance (Apr 11, 2023)
19-4682811-C-T		not specified	Uncertain significance (Jul 12, 2023)
19-4683563-C-T		not specified	Uncertain significance (Dec 02, 2024)
19-4683588-G-T		not specified	Uncertain significance (Jul 05, 2023)
19-4684663-C-T		Susceptibility to severe COVID-19	Likely pathogenic (Jul 22, 2024)
19-4684719-C-T		not specified	Uncertain significance (Nov 14, 2024)
19-4684722-C-T		not specified	Uncertain significance (Aug 17, 2021)
19-4684770-A-G			Likely benign (Dec 31, 2019)
19-4685634-C-T		not specified	Uncertain significance (Dec 18, 2023)
19-4685667-T-C		not specified	Uncertain significance (Mar 25, 2024)
19-4685682-C-T		not specified	Uncertain significance (May 26, 2024)
19-4685712-G-A		not specified	Uncertain significance (Mar 31, 2023)
19-4685724-G-A		not specified	Uncertain significance (Aug 17, 2022)
19-4685765-G-A		not specified	Uncertain significance (Sep 14, 2023)
19-4688787-G-T		not specified	Uncertain significance (Jun 22, 2023)
19-4688808-C-T		not specified	Uncertain significance (Aug 12, 2022)
19-4688812-G-T		not specified	Uncertain significance (Apr 23, 2024)
19-4688818-G-T			Benign (Aug 14, 2018)
19-4688838-G-A		not specified	Uncertain significance (Oct 05, 2023)
19-4688841-C-T		not specified	Uncertain significance (May 20, 2024)
19-4688859-C-T		not specified	Uncertain significance (Dec 27, 2023)
19-4688877-C-T		not specified	Likely benign (Sep 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DPP9	protein_coding	protein_coding	ENST00000262960	20	49450

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.987	0.0129	124627	0	13	124640	0.0000522

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.66	379	555	0.682	0.0000365	5802
Missense in Polyphen		138	234.38	0.58879		2483
Synonymous	-0.249	254	249	1.02	0.0000191	1676
Loss of Function	5.38	8	48.4	0.165	0.00000249	532

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.0000730	0.0000619
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Dipeptidyl peptidase that cleaves off N-terminal dipeptides from proteins having a Pro or Ala residue at position 2.
• Pathway: Lung fibrosis (Consensus)

Recessive Scores

• pRec: 0.179

Intolerance Scores

• loftool: 0.465
• rvis_EVS: -0.8
• rvis_percentile_EVS: 12.53

Haploinsufficiency Scores

• pHI: 0.389
• hipred: Y
• hipred_score: 0.768
• ghis: 0.602

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.984

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dpp9
• Phenotype: growth/size/body region phenotype; homeostasis/metabolism phenotype; muscle phenotype; craniofacial 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); digestive/alimentary phenotype

Gene ontology

• Biological process: proteolysis
• Cellular component: nucleus;cytosol
• Molecular function: aminopeptidase activity;serine-type peptidase activity;identical protein binding