DPT

dermatopontin

Basic information

Region (hg38): 1:168695468-168729206

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_specified (23 variants)
not_provided (11 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. These statistics are base on transcript: NM_000001937.5. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar	3 clinvar	5
missense	1 clinvar		23 clinvar	3 clinvar	3 clinvar	30
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	1	0	23	5	6

Highest pathogenic variant AF is 0.000027271533

Loading clinvar variants...

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