1-65309894-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001256864.2(DNAJC6):c.149C>T(p.Pro50Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000011 in 1,542,436 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001256864.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DNAJC6 | NM_001256864.2 | c.149C>T | p.Pro50Leu | missense_variant | Exon 1 of 19 | ENST00000371069.5 | NP_001243793.1 | |
DNAJC6 | NM_014787.4 | c.22+44962C>T | intron_variant | Intron 1 of 18 | NP_055602.1 | |||
DNAJC6 | NM_001256865.2 | c.-130-35717C>T | intron_variant | Intron 1 of 19 | NP_001243794.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152100Hom.: 0 Cov.: 30
GnomAD4 exome AF: 0.0000108 AC: 15AN: 1390336Hom.: 0 Cov.: 34 AF XY: 0.00000729 AC XY: 5AN XY: 685596
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152100Hom.: 0 Cov.: 30 AF XY: 0.0000135 AC XY: 1AN XY: 74274
ClinVar
Submissions by phenotype
Juvenile onset Parkinson disease 19A Uncertain:1
This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 50 of the DNAJC6 protein (p.Pro50Leu). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with DNAJC6-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at