chr3-132434209-CAAAAAAA-C
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_015268.4(DNAJC13):c.-13-323_-13-317delAAAAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000931 in 107,446 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.0000093 ( 0 hom., cov: 26)
Consequence
DNAJC13
NM_015268.4 intron
NM_015268.4 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.266
Genes affected
DNAJC13 (HGNC:30343): (DnaJ heat shock protein family (Hsp40) member C13) This gene encodes a member of the Dnaj protein family whose members act as co-chaperones of a partner heat-shock protein by binding to the latter and stimulating ATP hydrolysis. The encoded protein associates with the heat-shock protein Hsc70 and plays a role in clathrin-mediated endocytosis. It may also be involved in post-endocytic transport mechanisms via its associations with other proteins, including the sorting nexin SNX1. Mutations in this gene are associated with Parkinson's disease. [provided by RefSeq, Jun 2016]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DNAJC13 | NM_015268.4 | c.-13-323_-13-317delAAAAAAA | intron_variant | Intron 1 of 55 | ENST00000260818.11 | NP_056083.3 | ||
DNAJC13 | NM_001329126.2 | c.-13-323_-13-317delAAAAAAA | intron_variant | Intron 1 of 56 | NP_001316055.1 | |||
DNAJC13 | XM_047447819.1 | c.-13-323_-13-317delAAAAAAA | intron_variant | Intron 1 of 56 | XP_047303775.1 | |||
DNAJC13 | XM_047447820.1 | c.-13-323_-13-317delAAAAAAA | intron_variant | Intron 1 of 55 | XP_047303776.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DNAJC13 | ENST00000260818.11 | c.-13-328_-13-322delAAAAAAA | intron_variant | Intron 1 of 55 | 1 | NM_015268.4 | ENSP00000260818.6 | |||
DNAJC13 | ENST00000486798.5 | n.53-328_53-322delAAAAAAA | intron_variant | Intron 1 of 19 | 1 | |||||
DNAJC13 | ENST00000650455.1 | n.-13-328_-13-322delAAAAAAA | intron_variant | Intron 1 of 56 | ENSP00000496825.1 |
Frequencies
GnomAD3 genomes AF: 0.00000931 AC: 1AN: 107446Hom.: 0 Cov.: 26
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GnomAD4 genome AF: 0.00000931 AC: 1AN: 107446Hom.: 0 Cov.: 26 AF XY: 0.0000198 AC XY: 1AN XY: 50550
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at