DNAJC19

DnaJ heat shock protein family (Hsp40) member C19, the group of TIM23 complex|DNAJ (HSP40) heat shock proteins

Basic information

Region (hg38): 3:180983697-180989774

Links

ENSG00000205981 ∙ NCBI:131118 ∙ OMIM:608977 ∙ HGNC:30528 ∙ Uniprot:Q96DA6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• 3-methylglutaconic aciduria type 5 (Strong), mode of inheritance: AR
• 3-methylglutaconic aciduria type 5 (Supportive), mode of inheritance: AR
• 3-methylglutaconic aciduria type 5 (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
3-methylglutaconic aciduria, type V	AR	Cardiovascular	Individuals frequently demonstrate findings including cardiac manifestations such as dilated cardiomyopathy and dysrhythmias, and surveillance may allow early detection and management	Biochemical; Cardiovascular; Gastrointestinal; Genitourinary; Hematologic; Neurologic; Ophthalmologic	16055927; 22981120

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DNAJC19 gene.

• 3-methylglutaconic_aciduria_type_5 (116 variants)
• not_provided (23 variants)
• Inborn_genetic_diseases (15 variants)
• not_specified (12 variants)
• DNAJC19-related_disorder (4 variants)
• 3-Methylglutaconic_aciduria (1 variants)
• 3-Methylglutaconic_aciduria_type_3 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DNAJC19 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000145261.4. 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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				23		23
missense		1	38	4		43
nonsense	3					3
start loss			2			2
frameshift	7	2	3			12
splice donor/acceptor (+/-2bp)	1	6	2	1		10
Total	11	9	45	28	0

Highest pathogenic variant AF is 0.000041512492

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DNAJC19	protein_coding	protein_coding	ENST00000382564	6	6066

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000613	0.741	125696	0	52	125748	0.000207

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.876	44	63.7	0.691	0.00000336	747
Missense in Polyphen		8	14.931	0.5358		197
Synonymous	0.152	18	18.8	0.955	9.07e-7	216
Loss of Function	0.934	6	9.03	0.664	5.47e-7	97

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000570	0.000570
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000976	0.000971
European (Non-Finnish)	0.000123	0.000123
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable component of the PAM complex, a complex required for the translocation of transit peptide-containing proteins from the inner membrane into the mitochondrial matrix in an ATP-dependent manner. May act as a co-chaperone that stimulate the ATP-dependent activity (By similarity). {ECO:0000250}.
• Pathway: Metabolism of proteins;Mitochondrial protein import (Consensus)

Recessive Scores

• pRec: 0.142

Intolerance Scores

• loftool: 0.672
• rvis_EVS: -0.08
• rvis_percentile_EVS: 47.79

Haploinsufficiency Scores

• pHI: 0.247
• hipred: Y
• hipred_score: 0.788
• ghis: 0.648

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dnajc19
• Phenotype: homeostasis/metabolism phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: protein folding;protein targeting to mitochondrion;visual perception;protein import into mitochondrial matrix;positive regulation of ATPase activity;genitalia development
• Cellular component: PAM complex, Tim23 associated import motor;mitochondrion;mitochondrial inner membrane;integral component of membrane;protein-containing complex
• Molecular function: ATPase activator activity;protein binding;protein transporter activity