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

Genomes: not found (cov: 22)
Exomes 𝑓: 0.0000046 ( 0 hom. 2 hem. )

Consequence

DRP2
NM_001939.3 stop_gained

Scores

3
1
1

Clinical Significance

Uncertain significance criteria provided, single submitter U:2

Conservation

PhyloP100: 7.17
Variant links:
Genes affected
DRP2 (HGNC:3032): (dystrophin related protein 2) Members of the dystrophin family of proteins perform a critical role in the maintenance of membrane-associated complexes at points of intercellular contact in vertebrate cells. The protein encoded by this gene is predicted to resemble certain short C-terminal isoforms of dystrophin and dystrophin-related protein 1 (DRP1 or utrophin). DRP2 is expressed principally in the brain and spinal cord. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2010]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_pathogenic. Variant got 7 ACMG points.

PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
BS2
High Hemizygotes in GnomAdExome4 at 2 geneVariant has number of hemizygotes lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
DRP2NM_001939.3 linkc.1039C>T p.Gln347* stop_gained Exon 9 of 24 ENST00000395209.8 NP_001930.2 Q13474-1A0A024RCH3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DRP2ENST00000395209.8 linkc.1039C>T p.Gln347* stop_gained Exon 9 of 24 1 NM_001939.3 ENSP00000378635.3 Q13474-1

Frequencies

GnomAD3 genomes
Cov.:
22
GnomAD3 exomes
AF:
0.00000546
AC:
1
AN:
183190
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
67658
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000122
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000455
AC:
5
AN:
1097731
Hom.:
0
Cov.:
29
AF XY:
0.00000551
AC XY:
2
AN XY:
363097
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000475
Gnomad4 OTH exome
AF:
0.0000217
GnomAD4 genome
Cov.:
22
Alfa
AF:
0.000102
Hom.:
0
Bravo
AF:
0.00000756

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:2
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Uncertain:1
Nov 17, 2015
OMIM
Significance: Uncertain significance
Review Status: no assertion criteria provided
Collection Method: literature only

- -

Charcot-Marie-Tooth disease X-linked dominant 1 Uncertain:1
May 05, 2025
Concord Molecular Medicine Laboratory, Concord Repatriation General Hospital
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
0.62
D
BayesDel_noAF
Pathogenic
0.65
CADD
Pathogenic
38
DANN
Uncertain
1.0
FATHMM_MKL
Pathogenic
0.98
D
Vest4
0.92
GERP RS
5.5

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.27
Details are displayed if max score is > 0.2
DS_DL_spliceai
0.27
Position offset: 15

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1057519071; hg19: chrX-100497956; API