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

ENSG00000134146 ∙ NCBI:89978 ∙ OMIM:618391 ∙ HGNC:30543 ∙ Uniprot:Q7L8W6 ∙ 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 DPH6 gene.

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.

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			11	1	1	13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	1	1

Variants in DPH6

This is a list of pathogenic ClinVar variants found in the DPH6 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
15-35372172-G-C		not specified	Uncertain significance (May 27, 2022)
15-35373555-T-C		not specified	Uncertain significance (Jan 26, 2022)
15-35381867-T-C		not specified	Uncertain significance (May 15, 2023)
15-35381888-C-T		not specified	Uncertain significance (Oct 05, 2021)
15-35410843-G-A		not specified	Uncertain significance (Apr 07, 2022)
15-35410884-T-G		not specified	Uncertain significance (Oct 04, 2024)
15-35410885-C-G		not specified	Uncertain significance (Jun 04, 2024)
15-35450686-C-A		not specified	Uncertain significance (May 30, 2022)
15-35450709-T-C		not specified	Likely benign (Oct 26, 2022)
15-35454765-C-T		not specified	Uncertain significance (Nov 13, 2024)
15-35538324-A-G		not specified	Uncertain significance (May 30, 2023)
15-35538352-G-C		not specified	Uncertain significance (Oct 06, 2024)
15-35538360-C-T		not specified	Uncertain significance (Dec 28, 2022)
15-35538439-C-T		not specified	Uncertain significance (Oct 30, 2023)
15-35538450-C-T		not specified	Uncertain significance (Aug 30, 2021)
15-35538464-C-T			Benign (Dec 31, 2019)
15-35546129-C-A		not specified	Uncertain significance (Apr 01, 2024)
15-35546138-T-A		not specified	Uncertain significance (Sep 03, 2024)

GnomAD

Source: gnomAD

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: 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

• 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_gene_trap: N

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