rs869025615
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_000551.4(VHL):c.163del(p.Glu55ArgfsTer12) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 33)
Consequence
VHL
NM_000551.4 frameshift
NM_000551.4 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 3.15
Genes affected
VHL (HGNC:12687): (von Hippel-Lindau tumor suppressor) This gene encodes a component of a ubiquitination complex. The encoded protein is involved in the ubiquitination and degradation of hypoxia-inducible-factor (HIF), which is a transcription factor that plays a central role in the regulation of gene expression by oxygen. In addition to oxygen-related gene expression, this protein plays a role in many other cellular processes including cilia formation, cytokine signaling, regulation of senescence, and formation of the extracellular matrix. Variants of this gene are associated with von Hippel-Lindau syndrome, pheochromocytoma, erythrocytosis, renal cell carcinoma, and cerebellar hemangioblastoma. [provided by RefSeq, Jun 2022]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 12 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 3-10142008-TG-T is Pathogenic according to our data. Variant chr3-10142008-TG-T is described in ClinVar as [Pathogenic]. Clinvar id is 428800.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VHL | NM_000551.4 | c.163del | p.Glu55ArgfsTer12 | frameshift_variant | 1/3 | ENST00000256474.3 | |
VHL | NM_001354723.2 | c.163del | p.Glu55ArgfsTer12 | frameshift_variant | 1/3 | ||
VHL | NM_198156.3 | c.163del | p.Glu55ArgfsTer12 | frameshift_variant | 1/2 | ||
VHL | NR_176335.1 | n.233del | non_coding_transcript_exon_variant | 1/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VHL | ENST00000256474.3 | c.163del | p.Glu55ArgfsTer12 | frameshift_variant | 1/3 | 1 | NM_000551.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 genomes
?
Cov.:
33
GnomAD4 exome Cov.: 32
GnomAD4 exome
Cov.:
32
GnomAD4 genome ? Cov.: 33
GnomAD4 genome
?
Cov.:
33
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Hereditary cancer-predisposing syndrome Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 23, 2016 | The c.163delG pathogenic mutation, located in coding exon 1 of the VHL gene, results from a deletion of one nucleotide at nucleotide position 163, causing a translational frameshift with a predicted alternate stop codon. This mutation, designated as 376delG, has been reported in an individual with clinical features of von Hippel-Lindau syndrome (VHL) (Chen F et al. Hum. Mutat., 1995;5:66-75). Additionally, mRNA studies in Drosophila strains with this mutation confirmed that this frameshift alteration triggers nonsense-mediated decay (Micale L et al. J. Biomed. Biotechnol., 2009 Jan;2009:860761). This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation. - |
Computational scores
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at