DNAJC13

DnaJ heat shock protein family (Hsp40) member C13, the group of Armadillo like helical domain containing|DNAJ (HSP40) heat shock proteins

Basic information

Region (hg38): 3:132417502-132539032

Links

ENSG00000138246NCBI:23317OMIM:614334HGNC:30343Uniprot:O75165AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • hereditary late onset Parkinson disease (Supportive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Parkinson disease 21ADNeurologicResponse to levodopa has been describedNeurologic24218364; 25186792

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DNAJC13 gene.

  • not_specified (198 variants)
  • not_provided (71 variants)
  • DNAJC13-related_disorder (34 variants)
  • Parkinson_disease,_late-onset (2 variants)
  • Parkinson_disease_21 (2 variants)
  • Essential_tremor (1 variants)
  • Vascular_dementia (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DNAJC13 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000015268.4. 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
2
clinvar
17
clinvar
6
clinvar
25
missense
1
clinvar
205
clinvar
14
clinvar
8
clinvar
228
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 1 207 31 14

Highest pathogenic variant AF is 0.0000162313

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
DNAJC13protein_codingprotein_codingENST00000260818 55121507
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.002.49e-91257210261257470.000103
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.289451.16e+30.8120.000059114770
Missense in Polyphen142251.790.563963274
Synonymous0.7223834010.9540.00002064150
Loss of Function9.16171290.1310.000006881625

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0004270.000424
Ashkenazi Jewish0.00009920.0000992
East Asian0.0001630.000163
Finnish0.00004620.0000462
European (Non-Finnish)0.00008970.0000879
Middle Eastern0.0001630.000163
South Asian0.00003740.0000327
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Involved in membrane trafficking through early endosomes, such as the early endosome to recycling endosome transport implicated in the recycling of transferrin and the early endosome to late endosome transport implicated in degradation of EGF and EGFR (PubMed:18256511, PubMed:18307993). Involved in the regulation of endosomal membrane tubulation and regulates th dynamics of SNX1 on the endosomal membrane; via association with WASHC2 may link the WASH complex to the retromer SNX-BAR subcomplex (PubMed:24643499). {ECO:0000269|PubMed:18256511, ECO:0000269|PubMed:18307993, ECO:0000269|PubMed:24643499}.;
Disease
DISEASE: Parkinson disease (PARK) [MIM:168600]: A complex neurodegenerative disorder characterized by bradykinesia, resting tremor, muscular rigidity and postural instability. Additional features are characteristic postural abnormalities, dysautonomia, dystonic cramps, and dementia. The pathology of Parkinson disease involves the loss of dopaminergic neurons in the substantia nigra and the presence of Lewy bodies (intraneuronal accumulations of aggregated proteins), in surviving neurons in various areas of the brain. The disease is progressive and usually manifests after the age of 50 years, although early-onset cases (before 50 years) are known. The majority of the cases are sporadic suggesting a multifactorial etiology based on environmental and genetic factors. However, some patients present with a positive family history for the disease. Familial forms of the disease usually begin at earlier ages and are associated with atypical clinical features. {ECO:0000269|PubMed:24218364, ECO:0000269|PubMed:25393719}. Note=The gene represented in this entry may be involved in disease pathogenesis. Genetic variants in DNAJC13 (PubMed:24218364, PubMed:25393719) and TMEM230 (PubMed:27270108) have been found in the same large multigenerational family with adult-onset Parkinson disease. The pathological role of each gene and therefore the exact molecular basis of the disease is unclear. {ECO:0000305|PubMed:27270108}.;
Pathway
Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

pRec
0.139

Intolerance Scores

loftool
0.372
rvis_EVS
0.17
rvis_percentile_EVS
65.77

Haploinsufficiency Scores

pHI
0.418
hipred
N
hipred_score
0.476
ghis
0.568

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.781

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Dnajc13
Phenotype

Gene ontology

Biological process
osteoblast differentiation;receptor-mediated endocytosis;endosome organization;protein transport;neutrophil degranulation;regulation of early endosome to recycling endosome transport;regulation of early endosome to late endosome transport
Cellular component
lysosomal membrane;cytosol;plasma membrane;endosome membrane;membrane;secretory granule membrane;early endosome membrane;azurophil granule membrane;intracellular membrane-bounded organelle;extracellular exosome;WASH complex
Molecular function
protein binding