DPH3
Basic information
Region (hg38): 3:16257061-16264969
Previous symbols: [ "ZCSL2" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the DPH3 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 | 0 | |||||
| missense | 5 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 5 | 0 | 0 |
Variants in DPH3
This is a list of pathogenic ClinVar variants found in the DPH3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 3-16264162-T-C | not specified | Uncertain significance (Jul 09, 2024) | ||
| 3-16264198-G-T | not specified | Uncertain significance (Dec 02, 2024) | ||
| 3-16264795-A-G | not specified | Uncertain significance (Sep 22, 2022) | ||
| 3-16264806-T-C | not specified | Uncertain significance (Oct 06, 2021) | ||
| 3-16264816-T-A | not specified | Uncertain significance (Mar 21, 2024) | ||
| 3-16264824-T-C | not specified | Uncertain significance (Feb 09, 2025) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| DPH3 | protein_coding | protein_coding | ENST00000488423 | 3 | 6995 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0663 | 0.746 | 125710 | 0 | 7 | 125717 | 0.0000278 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.0913 | 44 | 42.3 | 1.04 | 0.00000184 | 545 |
| Missense in Polyphen | 11 | 13.301 | 0.82698 | 184 | ||
| Synonymous | -0.0529 | 16 | 15.7 | 1.02 | 7.40e-7 | 135 |
| Loss of Function | 0.891 | 2 | 3.90 | 0.513 | 1.63e-7 | 55 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000560 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000441 | 0.0000440 |
| Middle Eastern | 0.0000560 | 0.0000544 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Essential for the first step in the synthesis of diphthamide, a post-translational modification of histidine which occurs in elongation factor 2 (EEF2) and which can be ADP- ribosylated by diphtheria toxin and by Pseudomonas exotoxin A (Eta). {ECO:0000250}.;
- Pathway
- Post-translational protein modification;Metabolism of proteins;Synthesis of diphthamide-EEF2;Gamma carboxylation, hypusine formation and arylsulfatase activation
(Consensus)
Recessive Scores
- pRec
- 0.130
Intolerance Scores
- loftool
- 0.509
- rvis_EVS
- 0.1
- rvis_percentile_EVS
- 60.96
Haploinsufficiency Scores
- pHI
- 0.405
- hipred
- Y
- hipred_score
- 0.860
- ghis
- 0.621
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.617
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Dph3
- Phenotype
- growth/size/body region phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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); embryo phenotype;
Gene ontology
- Biological process
- tRNA wobble uridine modification;peptidyl-diphthamide biosynthetic process from peptidyl-histidine;negative regulation of protein secretion;positive regulation of binding
- Cellular component
- nucleus;nucleoplasm;cytoplasm;cytosol
- Molecular function
- protein binding;metal ion binding