DNAJC24

DnaJ heat shock protein family (Hsp40) member C24, the group of Diphthamide biosynthesis pathway genes|DNAJ (HSP40) heat shock proteins

Basic information

Region (hg38): 11:31369839-31432835

Previous symbols: [ "ZCSL3", "DPH4" ]

Links

ENSG00000170946 ∙ NCBI:120526 ∙ OMIM:611072 ∙ HGNC:26979 ∙ Uniprot:Q6P3W2 ∙ 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 DNAJC24 gene.

• Inborn genetic diseases (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DNAJC24 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			1			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	2	0	0

Variants in DNAJC24

This is a list of pathogenic ClinVar variants found in the DNAJC24 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-31414902-T-G		not specified	Uncertain significance (Feb 16, 2023)
11-31430328-A-G		not specified	Uncertain significance (Jul 14, 2022)
11-31430334-C-T		not specified	Uncertain significance (Dec 20, 2023)
11-31432522-C-A		not specified	Uncertain significance (Aug 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DNAJC24	protein_coding	protein_coding	ENST00000465995	4	62010

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.01e-7	0.132	124764	0	23	124787	0.0000922

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.660	59	75.1	0.786	0.00000349	978
Missense in Polyphen		16	23.348	0.68529		320
Synonymous	0.843	21	26.5	0.792	0.00000137	259
Loss of Function	-0.376	9	7.86	1.14	3.31e-7	103

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000183	0.000183
Ashkenazi Jewish	0.000302	0.000298
East Asian	0.000225	0.000223
Finnish	0.00	0.00
European (Non-Finnish)	0.0000621	0.0000618
Middle Eastern	0.000225	0.000223
South Asian	0.0000988	0.0000980
Other	0.000168	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Stimulates the ATPase activity of several Hsp70-type chaperones. This ability is enhanced by iron-binding. The iron- bound form is redox-active and can function as electron carrier. Plays a role in the 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:0000269|PubMed:22367199, ECO:0000269|PubMed:22509046}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Synthesis of diphthamide-EEF2;Gamma carboxylation, hypusine formation and arylsulfatase activation (Consensus)

Recessive Scores

• pRec: 0.125

Intolerance Scores

• loftool: 0.751
• rvis_EVS: 0.39
• rvis_percentile_EVS: 75.87

Haploinsufficiency Scores

• pHI: 0.0388
• hipred: N
• hipred_score: 0.204
• ghis: 0.498

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Dnajc24
• Phenotype: growth/size/body region phenotype; limbs/digits/tail phenotype; embryo phenotype; 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)

Gene ontology

• Biological process: peptidyl-diphthamide biosynthetic process from peptidyl-histidine;positive regulation of ATPase activity;oxidation-reduction process;chaperone-mediated protein folding
• Cellular component: cytoplasm;cytoskeleton
• Molecular function: ATPase activator activity;ferrous iron binding;zinc ion binding