13-52423602-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_016075.4(VPS36):c.812G>A(p.Cys271Tyr) variant causes a missense change. 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.812G>A | p.Cys271Tyr | missense_variant | Exon 10 of 14 | ENST00000378060.9 | NP_057159.2 | |
VPS36 | NM_001282168.2 | c.785G>A | p.Cys262Tyr | missense_variant | Exon 10 of 14 | NP_001269097.1 | ||
VPS36 | NM_001282169.2 | c.638G>A | p.Cys213Tyr | missense_variant | Exon 10 of 14 | NP_001269098.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VPS36 | ENST00000378060.9 | c.812G>A | p.Cys271Tyr | missense_variant | Exon 10 of 14 | 1 | NM_016075.4 | ENSP00000367299.3 | ||
VPS36 | ENST00000611132.4 | c.638G>A | p.Cys213Tyr | missense_variant | Exon 10 of 14 | 1 | ENSP00000484968.1 | |||
VPS36 | ENST00000650274.1 | n.812G>A | non_coding_transcript_exon_variant | Exon 10 of 15 | ENSP00000497484.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 29
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.812G>A (p.C271Y) alteration is located in exon 10 (coding exon 10) of the VPS36 gene. This alteration results from a G to A substitution at nucleotide position 812, causing the cysteine (C) at amino acid position 271 to be replaced by a tyrosine (Y). 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
Publications
No publications associated with this variant yet.