DPH6

diphthamine biosynthesis 6, the group of MicroRNA protein coding host genes|Diphthamide biosynthesis pathway genes

Basic information

Region (hg38): 15:35217345-35546193

Previous symbols: [ "ATPBD4" ]

Links

ENSG00000134146NCBI:89978OMIM:618391HGNC:30543Uniprot:Q7L8W6AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DPH6 gene.

  • 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.

EffectPLPVUSLBBSum
synonymous
0
missense
30
clinvar
2
clinvar
1
clinvar
33
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 30 2 1
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
DPH6protein_codingprotein_codingENST00000256538 9328849
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.00001140.8271257030371257400.000147
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.6141171370.8520.000006581732
Missense in Polyphen3040.2150.74599520
Synonymous-0.07694443.41.010.00000193479
Loss of Function1.341015.70.6368.11e-7201

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002830.000281
Ashkenazi Jewish0.000.00
East Asian0.0003290.000326
Finnish0.000.00
European (Non-Finnish)0.0001780.000176
Middle Eastern0.0003290.000326
South Asian0.0001000.0000980
Other0.0001660.000163

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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