rs201941494
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM1BS1_Supporting
The NM_016373.4(WWOX):c.946G>C(p.Val316Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000318 in 1,614,108 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V316A) has been classified as Uncertain significance.
Frequency
Consequence
NM_016373.4 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
WWOX | NM_016373.4 | c.946G>C | p.Val316Leu | missense_variant | 8/9 | ENST00000566780.6 | |
WWOX | NM_001291997.2 | c.607G>C | p.Val203Leu | missense_variant | 7/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
WWOX | ENST00000566780.6 | c.946G>C | p.Val316Leu | missense_variant | 8/9 | 1 | NM_016373.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000131 AC: 20AN: 152216Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000128 AC: 32AN: 249574Hom.: 0 AF XY: 0.000118 AC XY: 16AN XY: 135396
GnomAD4 exome AF: 0.000338 AC: 494AN: 1461892Hom.: 2 Cov.: 32 AF XY: 0.000334 AC XY: 243AN XY: 727248
GnomAD4 genome ? AF: 0.000131 AC: 20AN: 152216Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74354
ClinVar
Submissions by phenotype
Autosomal recessive spinocerebellar ataxia 12;C3463992:Developmental and epileptic encephalopathy, 1 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Dec 22, 2023 | This sequence change replaces valine, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 316 of the WWOX protein (p.Val316Leu). This variant is present in population databases (rs201941494, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with WWOX-related conditions. ClinVar contains an entry for this variant (Variation ID: 473036). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt WWOX protein function with a negative predictive value of 80%. 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. - |
Developmental and epileptic encephalopathy, 28 Other:1
not provided, no classification provided | phenotyping only | Department of Developmental Neurology, Medical University of Gdańsk | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at