DPT
Basic information
Region (hg38): 1:168695468-168729206
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- 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 | 5 | |||||
missense | 15 | |||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 1 | 0 | 8 | 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) | |||
1-168696586-C-T | not specified | Uncertain significance (Jun 04, 2024) | ||
1-168696611-G-A | Progressive sensorineural hearing impairment | Pathogenic (Mar 01, 2016) | ||
1-168701098-T-C | not specified | Uncertain significance (May 03, 2023) | ||
1-168714238-C-T | not specified | Likely benign (Apr 09, 2024) | ||
1-168714251-C-T | not specified | Uncertain significance (Mar 25, 2024) | ||
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) | |||
1-168714338-G-C | not specified | Uncertain significance (Sep 02, 2024) | ||
1-168728911-C-T | Benign (Dec 14, 2018) | |||
1-168728912-G-A | not specified | Uncertain significance (Aug 05, 2024) | ||
1-168728927-C-A | Likely benign (Dec 31, 2019) | |||
1-168728934-G-T | not specified | Uncertain significance (May 24, 2023) | ||
1-168728952-A-C | not specified | Uncertain significance (Jul 09, 2024) | ||
1-168728970-A-T | Likely benign (Dec 31, 2019) | |||
1-168729000-C-T | not specified | Uncertain significance (Sep 02, 2024) | ||
1-168729001-G-T | Benign (Dec 31, 2019) | |||
1-168729036-T-C | not specified | Uncertain significance (Mar 18, 2024) | ||
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) |
GnomAD
Source:
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:
- 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