3-119863457-C-A

Variant names:

• chr3-119863457-C-A
• rs2056136300
• NM_001146156.2:c.1058G>T

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2 PP3

The NM_001146156.2(GSK3B):​c.1058G>T​(p.Gly353Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: GSK3B NM_001146156.2 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 7.39

Genes affected

GSK3B (HGNC:4617): (glycogen synthase kinase 3 beta) The protein encoded by this gene is a serine-threonine kinase belonging to the glycogen synthase kinase subfamily. It is a negative regulator of glucose homeostasis and is involved in energy metabolism, inflammation, ER-stress, mitochondrial dysfunction, and apoptotic pathways. Defects in this gene have been associated with Parkinson disease and Alzheimer disease. [provided by RefSeq, Aug 2017]

ACMG classification

Verdict is Uncertain_significance. Variant got 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.79

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GSK3B	NM_001146156.2	c.1058G>T	p.Gly353Val	missense_variant	Exon 9 of 11	ENST00000264235.13	NP_001139628.1
GSK3B	NM_002093.4	c.1097G>T	p.Gly366Val	missense_variant	Exon 10 of 12		NP_002084.2
GSK3B	NM_001354596.2	c.1058G>T	p.Gly353Val	missense_variant	Exon 9 of 10		NP_001341525.1
GSK3B	XM_006713610.4	c.1097G>T	p.Gly366Val	missense_variant	Exon 10 of 11		XP_006713673.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GSK3B	ENST00000264235.13	c.1058G>T	p.Gly353Val	missense_variant	Exon 9 of 11	1	NM_001146156.2	ENSP00000264235.9

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

Bravo AF: 0.00000378

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Uncertain:1

Aug 27, 2022

GeneDx

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; Variants in candidate genes are classified as variants of uncertain significance in accordance with ACMG guidelines (Richards et al., 2015) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.81
BayesDel_addAF	Pathogenic	0.28	D
BayesDel_noAF	Pathogenic	0.16
CADD	Pathogenic	28
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.90	D;.;.
Eigen	Pathogenic	0.86
Eigen_PC	Pathogenic	0.83
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Pathogenic	0.99	D;D;D
M_CAP	Benign	0.056	D
MetaRNN	Pathogenic	0.79	D;D;D
MetaSVM	Benign	-0.43	T
MutationAssessor	Uncertain	2.6	M;.;.
PrimateAI	Pathogenic	0.80	D
PROVEAN	Pathogenic	-7.4	D;D;.
REVEL	Uncertain	0.55
Sift	Pathogenic	0.0	D;D;.
Sift4G	Uncertain	0.0070	D;D;.
Polyphen		0.98	D;D;.
Vest4		0.87
MutPred		0.46		Gain of glycosylation at T356 (P = 0.0216);.;Gain of glycosylation at T356 (P = 0.0216);
MVP		0.86
MPC		2.1
ClinPred		0.99	D
GERP RS		5.3
Varity_R		0.95
gMVP		0.78

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

Other links and lift over

dbSNP: rs2056136300; hg19: chr3-119582304;