DPT

dermatopontin

Basic information

Region (hg38): 1:168695467-168729206

Links

ENSG00000143196 ∙ NCBI:1805 ∙ OMIM:125597 ∙ HGNC:3011 ∙ Uniprot:Q07507 ∙ 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 DPT gene.

• not provided (11 variants)
• Inborn genetic diseases (7 variants)
• Progressive sensorineural hearing impairment (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DPT 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	1		7	3	3	14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	1	0	7	5	6

Highest pathogenic variant AF is 0.0000131

Variants in DPT

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

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

Position	Type	Phenotype	Significance	ClinVar
1-168696554-C-T			Benign (Dec 31, 2019)
1-168696573-G-A			Benign (Dec 31, 2019)
1-168696611-G-A		Progressive sensorineural hearing impairment	Pathogenic (Mar 01, 2016)
1-168701098-T-C		not specified	Uncertain significance (May 03, 2023)
1-168714252-G-A		not specified	Uncertain significance (Dec 18, 2023)
1-168714262-A-G			Likely benign (Mar 01, 2018)
1-168714275-C-T		not specified	Uncertain significance (Mar 22, 2023)
1-168714291-C-T			Benign (Dec 31, 2019)
1-168728911-C-T			Benign (Dec 14, 2018)
1-168728927-C-A			Likely benign (Dec 31, 2019)
1-168728934-G-T		not specified	Uncertain significance (May 24, 2023)
1-168728970-A-T			Likely benign (Dec 31, 2019)
1-168729000-C-T		not specified	Uncertain significance (Mar 22, 2022)
1-168729001-G-T			Benign (Dec 31, 2019)
1-168729047-C-T		not specified	Uncertain significance (Aug 14, 2023)
1-168729073-G-A			Likely benign (Dec 31, 2019)
1-168729073-G-T		not specified	Uncertain significance (Aug 21, 2023)
1-168729089-T-C		not specified	Uncertain significance (May 25, 2022)
1-168729167-A-G			Benign (Dec 31, 2019)
1-168729170-T-G			Likely benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DPT	protein_coding	protein_coding	ENST00000367817	4	33806

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000427	0.632	125714	0	34	125748	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0763	118	120	0.980	0.00000700	1331
Missense in Polyphen		29	35.931	0.8071		405
Synonymous	0.136	41	42.1	0.973	0.00000242	338
Loss of Function	0.951	10	13.8	0.724	6.80e-7	138

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000177	0.000177
Ashkenazi Jewish	0.000198	0.000198
East Asian	0.000163	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000159	0.000158
Middle Eastern	0.000163	0.000163
South Asian	0.000163	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Seems to mediate adhesion by cell surface integrin binding. May serve as a communication link between the dermal fibroblast cell surface and its extracellular matrix environment. Enhances TGFB1 activity. Inhibits cell proliferation. Accelerates collagen fibril formation, and stabilizes collagen fibrils against low-temperature dissociation (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.200

Intolerance Scores

• loftool: 0.769
• rvis_EVS: 0.68
• rvis_percentile_EVS: 85.04

Haploinsufficiency Scores

• pHI: 0.136
• hipred: Y
• hipred_score: 0.565
• ghis: 0.429

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.757

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dpt
• Phenotype: vision/eye phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Gene ontology

• Biological process: cell adhesion;negative regulation of cell population proliferation;collagen fibril organization
• Cellular component: extracellular space;collagen-containing extracellular matrix
• Molecular function: extracellular matrix structural constituent