DPH6
Basic information
Region (hg38): 15:35217345-35546193
Previous symbols: [ "ATPBD4" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (32 variants)
- not_provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the DPH6 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000080650.4. 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 | 0 | |||||
missense | 30 | 33 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 30 | 2 | 1 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
DPH6 | protein_coding | protein_coding | ENST00000256538 | 9 | 328849 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.0000114 | 0.827 | 125703 | 0 | 37 | 125740 | 0.000147 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.614 | 117 | 137 | 0.852 | 0.00000658 | 1732 |
Missense in Polyphen | 30 | 40.215 | 0.74599 | 520 | ||
Synonymous | -0.0769 | 44 | 43.4 | 1.01 | 0.00000193 | 479 |
Loss of Function | 1.34 | 10 | 15.7 | 0.636 | 8.11e-7 | 201 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000283 | 0.000281 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000329 | 0.000326 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.000178 | 0.000176 |
Middle Eastern | 0.000329 | 0.000326 |
South Asian | 0.000100 | 0.0000980 |
Other | 0.000166 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Amidase that catalyzes the last step of diphthamide biosynthesis using ammonium and ATP. Diphthamide biosynthesis consists in the conversion of an L-histidine residue in the translation elongation factor (EEF2) to diphthamide (By similarity). {ECO:0000250, ECO:0000269|PubMed:23169644}.;
- Pathway
- Post-translational protein modification;Metabolism of proteins;Synthesis of diphthamide-EEF2;Gamma carboxylation, hypusine formation and arylsulfatase activation;diphthamide biosynthesis
(Consensus)
Intolerance Scores
- loftool
- rvis_EVS
- 0.68
- rvis_percentile_EVS
- 84.93
Haploinsufficiency Scores
- pHI
- 0.296
- hipred
- N
- hipred_score
- 0.289
- ghis
- 0.453
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- gene_indispensability_score
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Dph6
- Phenotype
- 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); limbs/digits/tail phenotype; hematopoietic system phenotype; pigmentation phenotype; immune system phenotype; skeleton phenotype;
Gene ontology
- Biological process
- peptidyl-diphthamide biosynthetic process from peptidyl-histidine
- Cellular component
- nucleus;nucleolus;cytosol
- Molecular function
- ATP binding;diphthine-ammonia ligase activity