rs587780077
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PM1PM2PM5PP3_StrongPP5_Moderate
The NM_000551.4(VHL):c.445G>A(p.Ala149Thr) 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 Pathogenic (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A149S) has been classified as Pathogenic.
Frequency
Consequence
NM_000551.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
VHL | NM_000551.4 | c.445G>A | p.Ala149Thr | missense_variant | 2/3 | ENST00000256474.3 | |
VHL | NM_001354723.2 | c.*18-3169G>A | intron_variant | ||||
VHL | NM_198156.3 | c.341-3169G>A | intron_variant | ||||
VHL | NR_176335.1 | n.774G>A | non_coding_transcript_exon_variant | 3/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
VHL | ENST00000256474.3 | c.445G>A | p.Ala149Thr | missense_variant | 2/3 | 1 | NM_000551.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Von Hippel-Lindau syndrome Pathogenic:1
Pathogenic, no assertion criteria provided | clinical testing | Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia | Feb 26, 2016 | - - |
Hereditary cancer-predisposing syndrome Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 30, 2017 | The p.A149T pathogenic mutation (also known as c.445G>A), located in coding exon 2 of the VHL gene, results from a G to A substitution at nucleotide position 445. The alanine at codon 149 is replaced by threonine, an amino acid with similar properties. This alteration has been reported in individuals with a clinical diagnosis of von Hippel-Lindau (VHL) syndrome (Gallou C et al. Hum. Mutat., 2004 Sep;24:215-24; Ambry internal data). Functional analysis demonstrated a reduced affinity for and decreased ability to ubiquinate HIF-1α, a critical transcription factor activated during hypoxia, and regulated by VHL (Hansen WJ et al. Mol. Cell. Biol., 2002 Mar;22:1947-60). Based on internal structural analysis, this variant is anticipated to result in a significant decrease in structural stability (Van Molle I et al. Chem. Biol., 2012 Oct;19:1300-12). In addition, another alteration at this same amino acid position, p.A149S, has been shown to segregate with disease in two large VHL families (Mete T, et al. Endocrine 2014;45(1):128-35; Atuk NO, et al. J. Clin. Endocrinol. Metab. 1998;83(1):117-20). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at