DPH7

diphthamide biosynthesis 7, the group of WD repeat domain containing|Diphthamide biosynthesis pathway genes

Basic information

Region (hg38): 9:137554443-137578925

Previous symbols: [ "C9orf112", "WDR85" ]

Links

ENSG00000148399 ∙ NCBI:92715 ∙ OMIM:613210 ∙ HGNC:25199 ∙ Uniprot:Q9BTV6 ∙ 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 DPH7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DPH7 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			29	2		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	2	0

Variants in DPH7

This is a list of pathogenic ClinVar variants found in the DPH7 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-137555270-G-A		not specified	Likely benign (Jun 29, 2023)
9-137555285-G-A		not specified	Uncertain significance (Dec 01, 2022)
9-137555300-A-C		not specified	Uncertain significance (Oct 03, 2022)
9-137555316-C-T		not specified	Likely benign (Dec 06, 2022)
9-137555337-C-T		not specified	Uncertain significance (Dec 28, 2022)
9-137555369-A-G		not specified	Uncertain significance (Jan 26, 2022)
9-137555376-T-G		not specified	Uncertain significance (Mar 19, 2024)
9-137555484-C-T		not specified	Uncertain significance (Apr 08, 2023)
9-137555540-G-A		not specified	Uncertain significance (Aug 30, 2021)
9-137555562-G-A		not specified	Uncertain significance (Jun 28, 2022)
9-137555574-A-G		not specified	Uncertain significance (May 09, 2023)
9-137555591-T-C		not specified	Uncertain significance (Apr 18, 2023)
9-137555618-G-A		not specified	Uncertain significance (Apr 09, 2022)
9-137564451-T-C		Malignant tumor of prostate	Uncertain significance (-)
9-137564500-G-T		not specified	Uncertain significance (Jun 11, 2024)
9-137564539-G-C		not specified	Uncertain significance (May 25, 2022)
9-137564547-G-T		not specified	Uncertain significance (May 14, 2024)
9-137564574-C-T		not specified	Uncertain significance (Jan 22, 2024)
9-137564604-T-C		not specified	Uncertain significance (Feb 06, 2023)
9-137564911-T-C		not specified	Uncertain significance (Oct 27, 2022)
9-137565148-T-C		not specified	Uncertain significance (Mar 16, 2022)
9-137565149-C-T		not specified	Uncertain significance (Jul 20, 2022)
9-137565152-C-A		not specified	Uncertain significance (Mar 23, 2023)
9-137574256-C-T		not specified	Uncertain significance (Feb 22, 2023)
9-137574270-G-A		not specified	Uncertain significance (Feb 22, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DPH7	protein_coding	protein_coding	ENST00000277540	9	24032

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.86e-8	0.425	125699	0	49	125748	0.000195

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.000725	255	255	1.00	0.0000140	2949
Missense in Polyphen		61	66.987	0.91063		776
Synonymous	-0.504	117	110	1.06	0.00000679	887
Loss of Function	0.869	14	18.0	0.779	8.66e-7	196

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000609	0.000607
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000221	0.000220
Middle Eastern	0.000272	0.000272
South Asian	0.0000653	0.0000653
Other	0.000490	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Catalyzes the demethylation of diphthine methyl ester to form diphthine, an intermediate diphthamide biosynthesis, a post- translational modification of histidine which occurs in translation elongation factor 2 (EEF2) which can be ADP- ribosylated by diphtheria toxin and by Pseudomonas exotoxin A (Eta). {ECO:0000250|UniProtKB:P38332, ECO:0000269|PubMed:19965467, ECO:0000269|PubMed:23486472}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Synthesis of diphthamide-EEF2;Gamma carboxylation, hypusine formation and arylsulfatase activation (Consensus)

Intolerance Scores

• rvis_EVS: 0.24
• rvis_percentile_EVS: 69.46

Haploinsufficiency Scores

• pHI: 0.0908
• hipred: Y
• hipred_score: 0.521
• ghis: 0.447

Essentials

• essential_gene_CRISPR: N
• 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: Dph7

Gene ontology

• Biological process: peptidyl-diphthamide biosynthetic process from peptidyl-histidine
• Molecular function: protein binding;diphthine methylesterase activity