rs1057519071
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 8P and 1B. PVS1BS2_Supporting
The NM_001939.3(DRP2):c.1039C>T(p.Gln347*) variant causes a stop gained change. The variant allele was found at a frequency of 0.00000455 in 1,097,731 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 2 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001939.3 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DRP2 | NM_001939.3 | c.1039C>T | p.Gln347* | stop_gained | Exon 9 of 24 | ENST00000395209.8 | NP_001930.2 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 22
GnomAD3 exomes AF: 0.00000546 AC: 1AN: 183190Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67658
GnomAD4 exome AF: 0.00000455 AC: 5AN: 1097731Hom.: 0 Cov.: 29 AF XY: 0.00000551 AC XY: 2AN XY: 363097
GnomAD4 genome Cov.: 22
ClinVar
Submissions by phenotype
not provided Uncertain:1
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Charcot-Marie-Tooth disease X-linked dominant 1 Uncertain:1
This variant was detected in a male patient with adult-onset axonal sensorimotor neuropathy confirmed by nerve conduction study. This nucleotide change leads to a premature termination codon in exon 9 out of a total of 24 exons. The transcript is predicted to undergo nonsense mediated decay. This variant is found at a very low frequency in control population database (0.0004%, gnomAD v4.1.0). The same variant was described in two hemizygous case reports in patients with Charcot-Marie-Tooth disease. Other loss of function variants in DRP2 causing Charcot-Marie-Tooth disease have been described. While the variant level evidence suggests this variant to be likely pathogenic, the gene disease association remains to be established and therefore this variant is currently classified as a variant of uncertain significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at