Our verdict is Benign. Variant got -7 ACMG points: 1P and 8B. PP2BP4_StrongBS2
The NM_006044.4(HDAC6):c.51G>C(p.Arg17Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000389 in 1,207,114 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 16 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
HDAC6 (HGNC:14064): (histone deacetylase 6) Histones play a critical role in transcriptional regulation, cell cycle progression, and developmental events. Histone acetylation/deacetylation alters chromosome structure and affects transcription factor access to DNA. The protein encoded by this gene belongs to class II of the histone deacetylase/acuc/apha family. It contains an internal duplication of two catalytic domains which appear to function independently of each other. This protein possesses histone deacetylase activity and represses transcription. [provided by RefSeq, Jul 2008]
PP2 - Missense variant in a gene that has a low rate of benign missense variation and in which missense variants are a common mechanism of disease
Missense variant where missense usually causes diseases, HDAC6
BP4
?
BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (MetaRNN=0.02738434).
BS2
?
BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
Uncertain significance, criteria provided, single submitter
clinical testing
Ambry Genetics
Aug 13, 2021
The c.51G>C (p.R17S) alteration is located in exon 2 (coding exon 1) of the HDAC6 gene. This alteration results from a G to C substitution at nucleotide position 51, causing the arginine (R) at amino acid position 17 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Gain of phosphorylation at R17 (P = 6e-04);Gain of phosphorylation at R17 (P = 6e-04);Gain of phosphorylation at R17 (P = 6e-04);Gain of phosphorylation at R17 (P = 6e-04);Gain of phosphorylation at R17 (P = 6e-04);Gain of phosphorylation at R17 (P = 6e-04);Gain of phosphorylation at R17 (P = 6e-04);Gain of phosphorylation at R17 (P = 6e-04);Gain of phosphorylation at R17 (P = 6e-04);Gain of phosphorylation at R17 (P = 6e-04);Gain of phosphorylation at R17 (P = 6e-04);Gain of phosphorylation at R17 (P = 6e-04);Gain of phosphorylation at R17 (P = 6e-04);Gain of phosphorylation at R17 (P = 6e-04);Gain of phosphorylation at R17 (P = 6e-04);