X-72330062-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4BS1_Supporting
The NM_018486.3(HDAC8):c.1126G>A(p.Val376Met) variant causes a missense change. The variant allele was found at a frequency of 0.00000414 in 1,206,895 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_018486.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
HDAC8 | ENST00000373573.9 | c.1126G>A | p.Val376Met | missense_variant | Exon 11 of 11 | 1 | NM_018486.3 | ENSP00000362674.3 | ||
ENSG00000285547 | ENST00000648922.1 | c.1111+21671G>A | intron_variant | Intron 10 of 11 | ENSP00000497072.1 |
Frequencies
GnomAD3 genomes AF: 0.0000267 AC: 3AN: 112170Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34326
GnomAD4 exome AF: 0.00000183 AC: 2AN: 1094725Hom.: 0 Cov.: 27 AF XY: 0.00 AC XY: 0AN XY: 360203
GnomAD4 genome AF: 0.0000267 AC: 3AN: 112170Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34326
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.1126G>A (p.V376M) alteration is located in exon 11 (coding exon 11) of the HDAC8 gene. This alteration results from a G to A substitution at nucleotide position 1126, causing the valine (V) at amino acid position 376 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Cornelia de Lange syndrome 5 Uncertain:1
This sequence change replaces valine, which is neutral and non-polar, with methionine, which is neutral and non-polar, at codon 376 of the HDAC8 protein (p.Val376Met). This variant is present in population databases (no rsID available, gnomAD 0.009%). This variant has not been reported in the literature in individuals affected with HDAC8-related conditions. ClinVar contains an entry for this variant (Variation ID: 2142066). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt HDAC8 protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at