chr11-111908793-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_001289808.2(CRYAB):​c.499C>G​(p.Pro167Ala) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Consequence

CRYAB
NM_001289808.2 missense

Scores

8
11

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 3.95
Variant links:
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.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.28232348).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
CRYABNM_001289808.2 linkuse as main transcriptc.499C>G p.Pro167Ala missense_variant 3/3 ENST00000650687.2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
CRYABENST00000650687.2 linkuse as main transcriptc.499C>G p.Pro167Ala missense_variant 3/3 NM_001289808.2 P1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Dilated cardiomyopathy 1II Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingInvitaeFeb 19, 2021In 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. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals with CRYAB-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change replaces proline with alanine at codon 167 of the CRYAB protein (p.Pro167Ala). The proline residue is moderately conserved and there is a small physicochemical difference between proline and alanine. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.074
BayesDel_addAF
Uncertain
0.12
D
BayesDel_noAF
Uncertain
-0.060
CADD
Benign
22
DANN
Uncertain
0.98
DEOGEN2
Uncertain
0.59
D;T;T;D;D;D;D;D;T;T;.
Eigen
Benign
-0.056
Eigen_PC
Benign
0.13
FATHMM_MKL
Uncertain
0.95
D
LIST_S2
Benign
0.84
.;.;.;T;.;.;.;.;T;.;T
M_CAP
Benign
0.027
D
MetaRNN
Benign
0.28
T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Uncertain
0.28
D
MutationAssessor
Benign
1.0
L;.;.;L;L;L;L;L;.;.;.
MutationTaster
Benign
0.97
D;D;D;D;D;D;D
PrimateAI
Uncertain
0.52
T
PROVEAN
Uncertain
-3.1
D;D;D;.;D;D;D;D;D;D;D
REVEL
Benign
0.24
Sift
Benign
0.038
D;D;D;.;D;D;D;D;D;T;T
Sift4G
Benign
0.18
T;T;T;T;T;T;T;T;.;.;.
Polyphen
0.0030
B;.;.;B;B;B;B;B;.;.;.
Vest4
0.27
MutPred
0.25
Gain of MoRF binding (P = 0.0409);.;.;Gain of MoRF binding (P = 0.0409);Gain of MoRF binding (P = 0.0409);Gain of MoRF binding (P = 0.0409);Gain of MoRF binding (P = 0.0409);Gain of MoRF binding (P = 0.0409);.;Gain of MoRF binding (P = 0.0409);.;
MVP
0.99
MPC
0.25
ClinPred
0.77
D
GERP RS
5.1
Varity_R
0.37
gMVP
0.36

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1965354125; hg19: chr11-111779517; API