13-52436301-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_016075.4(VPS36):c.340G>T(p.Gly114Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_016075.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VPS36 | NM_016075.4 | c.340G>T | p.Gly114Cys | missense_variant | Exon 4 of 14 | ENST00000378060.9 | NP_057159.2 | |
VPS36 | NM_001282168.2 | c.313G>T | p.Gly105Cys | missense_variant | Exon 4 of 14 | NP_001269097.1 | ||
VPS36 | NM_001282169.2 | c.166G>T | p.Gly56Cys | missense_variant | Exon 4 of 14 | NP_001269098.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000404 AC: 1AN: 247568Hom.: 0 AF XY: 0.00000749 AC XY: 1AN XY: 133534
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1457682Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 724842
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.340G>T (p.G114C) alteration is located in exon 4 (coding exon 4) of the VPS36 gene. This alteration results from a G to T substitution at nucleotide position 340, causing the glycine (G) at amino acid position 114 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at