chr11-111908781-C-T
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_001289808.2(CRYAB):c.511G>A(p.Ala171Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000105 in 1,612,654 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A171S) has been classified as Uncertain significance.
Frequency
Consequence
NM_001289808.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CRYAB | NM_001289808.2 | c.511G>A | p.Ala171Thr | missense_variant | 3/3 | ENST00000650687.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRYAB | ENST00000650687.2 | c.511G>A | p.Ala171Thr | missense_variant | 3/3 | NM_001289808.2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152142Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251444Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135894
GnomAD4 exome AF: 0.0000110 AC: 16AN: 1460512Hom.: 0 Cov.: 31 AF XY: 0.0000151 AC XY: 11AN XY: 726586
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152142Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74350
ClinVar
Submissions by phenotype
Dilated cardiomyopathy 1II Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Nov 01, 2022 | This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 171 of the CRYAB protein (p.Ala171Thr). This variant is present in population databases (rs370803064, gnomAD 0.007%). This missense change has been observed in individuals with clinical features of autosomal dominant myofibrillar myopathy and/or congenital cataracts (PMID: 18587492; Invitae). ClinVar contains an entry for this variant (Variation ID: 381526). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. Experimental studies have shown that this missense change affects CRYAB function (PMID: 23194663, 32110827). 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. - |
Cardiomyopathy Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario | Sep 09, 2016 | - - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Jan 03, 2017 | A variant of uncertain significance has been identified in the CRYAB gene. Although the A171T variant has not been published in association with DCM, it has been reported in one pediatric patient with cataracts and was inherited from his father who was not evaluated for cataracts (Devi et al., 2008). This variant was not observed with any significant frequency in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project. The A171T variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties.Functional studies using cells transfected with the A171T variant showed an increase in apoptosis compared to wild type cells (Raju et al., 2013); however, it is not known whether these findings are biological or clinically relevant in vivo. The A171T substitution occurs at a position that is only conserved in mammals and in silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. Therefore, based on the currently available information, it is unclear whether this variant is pathogenic or rare benign. This result cannot be interpreted for diagnosis or used for family member screening at this time. - |
Cardiovascular phenotype Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 01, 2023 | The p.A171T variant (also known as c.511G>A), located in coding exon 3 of the CRYAB gene, results from a G to A substitution at nucleotide position 511. The alanine at codon 171 is replaced by threonine, an amino acid with similar properties. This variant has been detected in a proband with congenital cataracts and in the reportedly unaffected father (Devi RR et al. Mol Vis, 2008 Jun;14:1157-70). This variant was also detected in an individual from an exome sequencing cohort not selected for the presence of cardiovascular disease or cataracts; however, details were limited (Kars ME et al. Proc Natl Acad Sci U S A, 2021 Sep;118). Functional studies suggest this variant may lead to aggregate formation and apoptosis in transfected cells; however, the clinical relevance of these findings are unclear (Raju I et al. Biochem Biophys Res Commun, 2013 Jan;430:107-12). This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at