chr6-3224918-G-A
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM2PM5PP2PP3_StrongPP5_Moderate
The NM_178012.5(TUBB2B):c.1171C>T(p.Arg391Cys) 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 Likely pathogenic (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R391H) has been classified as Likely pathogenic.
Frequency
Consequence
NM_178012.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TUBB2B | NM_178012.5 | c.1171C>T | p.Arg391Cys | missense_variant | 4/4 | ENST00000259818.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TUBB2B | ENST00000259818.8 | c.1171C>T | p.Arg391Cys | missense_variant | 4/4 | 1 | NM_178012.5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 20
GnomAD4 exome Cov.: 32
GnomAD4 genome ? Cov.: 20
ClinVar
Submissions by phenotype
not provided Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Aug 28, 2023 | In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Not observed at significant frequency in large population cohorts (gnomAD); Missense variants in this gene are often considered pathogenic (HGMD); Previously reported as a de novo variant in an individual with DandyWalker malformation and anterior commissure agenesis as well as dysmorphic facial features; an inherited variant in another gene associated with this phenotype was also observed (Dawidziuk et al., 2021); This variant is associated with the following publications: (PMID: 27010057, Vita[book]2021, 34946966) - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.