rs281865142
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Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 5P and 4B. PVS1_StrongPP5BS2
The NM_001289808.2(CRYAB):c.343del(p.Ser115ProfsTer14) variant causes a frameshift change. The variant allele was found at a frequency of 0.00000991 in 1,613,966 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000096 ( 0 hom. )
Consequence
CRYAB
NM_001289808.2 frameshift
NM_001289808.2 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 5.29
Genes affected
CRYAB (HGNC:2389): (crystallin alpha B) Mammalian lens crystallins are divided into alpha, beta, and gamma families. Alpha crystallins are composed of two gene products: alpha-A and alpha-B, for acidic and basic, respectively. Alpha crystallins can be induced by heat shock and are members of the small heat shock protein (HSP20) family. They act as molecular chaperones although they do not renature proteins and release them in the fashion of a true chaperone; instead they hold them in large soluble aggregates. These heterogeneous aggregates consist of 30-40 subunits; the alpha-A and alpha-B subunits have a 3:1 ratio, respectively. Two additional functions of alpha crystallins are an autokinase activity and participation in the intracellular architecture. The encoded protein has been identified as a moonlighting protein based on its ability to perform mechanistically distinct functions. Alpha-A and alpha-B gene products are differentially expressed; alpha-A is preferentially restricted to the lens and alpha-B is expressed widely in many tissues and organs. Elevated expression of alpha-B crystallin occurs in many neurological diseases; a missense mutation cosegregated in a family with a desmin-related myopathy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2019]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PVS1
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. There are 10 pathogenic variants in the truncated region.
PP5
Variant 11-111908948-GA-G is Pathogenic according to our data. Variant chr11-111908948-GA-G is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 38963.We mark this variant Likely_pathogenic, oryginal submissions are: {Likely_pathogenic=1, not_provided=1, Uncertain_significance=1, Pathogenic=4}.
BS2
High AC in GnomAdExome4 at 14 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CRYAB | NM_001289808.2 | c.343del | p.Ser115ProfsTer14 | frameshift_variant | 3/3 | ENST00000650687.2 | NP_001276737.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CRYAB | ENST00000650687.2 | c.343del | p.Ser115ProfsTer14 | frameshift_variant | 3/3 | NM_001289808.2 | ENSP00000499082 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152104Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250916Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135704
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GnomAD4 exome AF: 0.00000958 AC: 14AN: 1461862Hom.: 0 Cov.: 31 AF XY: 0.00000825 AC XY: 6AN XY: 727236
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GnomAD4 genome AF: 0.0000131 AC: 2AN: 152104Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74312
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Pathogenic:5Uncertain:1Other:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not provided Pathogenic:3
Pathogenic, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Feb 09, 2023 | - - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Aug 08, 2018 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Sep 09, 2021 | Not observed at a significant frequency in large population cohorts (Lek et al., 2016); Frameshift variant predicted to result in protein truncation, as the last 61 amino acids are replaced with 13 different amino acids, and other loss-of-function variants have been reported downstream in the Human Gene Mutation Database (Stenson et al., 2014); Published functional studies demonstrate a damaging effect as induced pluripotent stem cells (iPSC) derived from fibroblasts from an infant with myofibrillar myopathy showed that this variant causes protein insolubility, resulting in the loss of alpha-B-crystallin protein expression in iPSC-derived skeletal myotubes and cardiomyocytes (Mitzelfelt et al., 2016); Reported in ClinVar (ClinVar Variant ID# 38963; Landrum et al., 2016); While other truncating variants in the CRYAB gene have been reported in HGMD in association with autosomal recessive infantile myofibrillar myopathy (Stenson et al., 2014), only one truncating variant has been previously reported in association with autosomal dominant cardiomyopathy (Jensen et al. 2013).; This variant is associated with the following publications: (PMID: 21130652, 27226619, 31534214) - |
Dilated cardiomyopathy 1II Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 01, 2024 | This sequence change creates a premature translational stop signal (p.Ser115Profs*14) in the CRYAB gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 61 amino acid(s) of the CRYAB protein. This variant is present in population databases (rs281865142, gnomAD no frequency). This premature translational stop signal has been observed in individuals with autosomal recessive myofibrillar myopathy (PMID: 21130652, 27226619). ClinVar contains an entry for this variant (Variation ID: 38963). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this premature translational stop signal affects CRYAB function (PMID: 21130652, 27226619). For these reasons, this variant has been classified as Pathogenic. - |
Myofibrillar myopathy 2;C3554649:Dilated cardiomyopathy 1II;C3808377:Cataract 16 multiple types;C5190691:Fatal infantile hypertonic myofibrillar myopathy Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Aug 27, 2021 | - - |
Cardiovascular phenotype Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 03, 2021 | The c.343delT (p.S115Pfs*14) alteration, located in exon 3 (coding exon 3) of the CRYAB gene, consists of a deletion of one nucleotide at position 343, causing a translational frameshift with a predicted alternate stop codon after 14 amino acids. Frameshift alterations are typically deleterious in nature (Richards, 2015). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Myofibrillar myopathy 2 Other:1
not provided, no classification provided | literature only | GeneReviews | - | - - |
Computational scores
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at