chr20-2860242-AAGAGTGGACCCGTGG-GAGAGC
Position:
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1PM2PP5
The NM_022575.4(VPS16):c.244_259delinsGAGAGC(p.Lys82GlufsTer126) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Consequence
VPS16
NM_022575.4 frameshift
NM_022575.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 8.58
Genes affected
VPS16 (HGNC:14584): (VPS16 core subunit of CORVET and HOPS complexes) Vesicle mediated protein sorting plays an important role in segregation of intracellular molecules into distinct organelles. Genetic studies in yeast have identified more than 40 vacuolar protein sorting (VPS) genes involved in vesicle transport to vacuoles. This gene encodes the human homolog of yeast class C Vps16 protein. The mammalian class C Vps proteins are predominantly associated with late endosomes/lysosomes, and like their yeast counterparts, may mediate vesicle trafficking steps in the endosome/lysosome pathway. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2009]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 11 ACMG points.
PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 20-2860242-AAGAGTGGACCCGTGG-GAGAGC is Pathogenic according to our data. Variant chr20-2860242-AAGAGTGGACCCGTGG-GAGAGC is described in ClinVar as [Pathogenic]. Clinvar id is 1065417.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
VPS16 | NM_022575.4 | c.244_259delinsGAGAGC | p.Lys82GlufsTer126 | frameshift_variant | 4/24 | ENST00000380445.8 | NP_072097.2 | |
VPS16 | NM_080413.3 | c.244_259delinsGAGAGC | p.Lys82GlufsTer126 | frameshift_variant | 4/20 | NP_536338.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VPS16 | ENST00000380445.8 | c.244_259delinsGAGAGC | p.Lys82GlufsTer126 | frameshift_variant | 4/24 | 1 | NM_022575.4 | ENSP00000369810 | P1 | |
VPS16 | ENST00000380469.7 | c.244_259delinsGAGAGC | p.Lys82GlufsTer126 | frameshift_variant | 4/20 | 2 | ENSP00000369836 | |||
VPS16 | ENST00000417508.1 | c.16-207_16-192delinsGAGAGC | intron_variant | 5 | ENSP00000409840 | |||||
VPS16 | ENST00000453689.5 | c.16-207_16-192delinsGAGAGC | intron_variant | 3 | ENSP00000417031 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Dystonia 30 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Oct 20, 2021 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.