X-101231690-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 5P and 1B. PVS1_StrongPP5BS2_Supporting

The NM_001939.3(DRP2):​c.43C>T​(p.Arg15*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,098,084 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 4 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: not found (cov: 22)
Exomes 𝑓: 0.000012 ( 0 hom. 4 hem. )

Consequence

DRP2
NM_001939.3 stop_gained

Scores

2
2
1

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1U:1

Conservation

PhyloP100: 2.31
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 Uncertain_significance. Variant got 4 ACMG points.

PVS1
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant located near the start codon (<100nt), not predicted to undergo nonsense mediated mRNA decay. Fraction of 0.985 CDS is truncated, and there are 0 pathogenic variants in the truncated region.
PP5
Variant X-101231690-C-T is Pathogenic according to our data. Variant chrX-101231690-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 807792.We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=1, Pathogenic=1}.
BS2
High Hemizygotes in GnomAdExome4 at 4 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.43C>T p.Arg15* stop_gained Exon 3 of 24 ENST00000395209.8 NP_001930.2 Q13474-1A0A024RCH3
DRP2XM_047441894.1 linkc.43C>T p.Arg15* stop_gained Exon 2 of 23 XP_047297850.1
DRP2XM_017029333.2 linkc.43C>T p.Arg15* stop_gained Exon 3 of 23 XP_016884822.1
DRP2NM_001171184.2 linkc.-117-4170C>T intron_variant Intron 1 of 21 NP_001164655.1 Q13474-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
DRP2ENST00000395209.8 linkc.43C>T p.Arg15* stop_gained Exon 3 of 24 1 NM_001939.3 ENSP00000378635.3 Q13474-1

Frequencies

GnomAD3 genomes
Cov.:
22
GnomAD3 exomes
AF:
0.00000546
AC:
1
AN:
183150
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
67642
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:
0.0000118
AC:
13
AN:
1098084
Hom.:
0
Cov.:
30
AF XY:
0.0000110
AC XY:
4
AN XY:
363448
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000284
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:
0.0000143
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
22
ExAC
AF:
0.00000824
AC:
1
EpiCase
AF:
0.00
EpiControl
AF:
0.0000594

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Pathogenic:1Uncertain:1
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

not provided Pathogenic:1Uncertain:1
Pathogenic, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpNov 05, 2023This sequence change creates a premature translational stop signal (p.Arg15*) in the DRP2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in DRP2 are known to be pathogenic (PMID: 22764250, 26227883). This variant is present in population databases (rs756695526, gnomAD 0.001%). This variant has not been reported in the literature in individuals affected with DRP2-related conditions. ClinVar contains an entry for this variant (Variation ID: 807792). For these reasons, this variant has been classified as Pathogenic. -
Uncertain significance, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenOct 01, 2022DRP2: PM2 -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
0.57
D
BayesDel_noAF
Pathogenic
0.59
CADD
Pathogenic
35
DANN
Uncertain
1.0
FATHMM_MKL
Uncertain
0.84
D
Vest4
0.77
GERP RS
5.0

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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: rs756695526; hg19: chrX-100486679; API