chr20-2860242-AAGAGTGGACCCGTGG-GAGAGC

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

Scores

Not classified

Clinical Significance

Pathogenic no assertion criteria provided P:1

Conservation

PhyloP100: 8.58
Variant links:
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]

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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
VPS16NM_022575.4 linkuse as main transcriptc.244_259delinsGAGAGC p.Lys82GlufsTer126 frameshift_variant 4/24 ENST00000380445.8 NP_072097.2
VPS16NM_080413.3 linkuse as main transcriptc.244_259delinsGAGAGC p.Lys82GlufsTer126 frameshift_variant 4/20 NP_536338.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
VPS16ENST00000380445.8 linkuse as main transcriptc.244_259delinsGAGAGC p.Lys82GlufsTer126 frameshift_variant 4/241 NM_022575.4 ENSP00000369810 P1Q9H269-1
VPS16ENST00000380469.7 linkuse as main transcriptc.244_259delinsGAGAGC p.Lys82GlufsTer126 frameshift_variant 4/202 ENSP00000369836 Q9H269-2
VPS16ENST00000417508.1 linkuse as main transcriptc.16-207_16-192delinsGAGAGC intron_variant 5 ENSP00000409840
VPS16ENST00000453689.5 linkuse as main transcriptc.16-207_16-192delinsGAGAGC intron_variant 3 ENSP00000417031

Frequencies

GnomAD3 genomes
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
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 providedliterature onlyOMIMOct 20, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr20-2840888; API