9-132897323-T-C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_000368.5(TSC1):​c.2836A>G​(p.Ser946Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. 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

TSC1
NM_000368.5 missense

Scores

10
9

Clinical Significance

Uncertain significance criteria provided, multiple submitters, no conflicts U:2

Conservation

PhyloP100: 3.41
Variant links:
Genes affected
TSC1 (HGNC:12362): (TSC complex subunit 1) This gene is a tumor suppressor gene that encodes the growth inhibitory protein hamartin. The encoded protein interacts with and stabilizes the GTPase activating protein tuberin. This hamartin-tuberin complex negatively regulates mammalian target of rapamycin complex 1 (mTORC1) signaling which is a major regulator of anabolic cell growth. This protein also functions as a co-chaperone for Hsp90 that inhibits its ATPase activity. This protein functions as a facilitator of Hsp90-mediated folding of kinase and non-kinase clients, including TSC2 and thereby preventing their ubiquitination and proteasomal degradation. Mutations in this gene have been associated with tuberous sclerosis and lymphangioleiomyomatosis. [provided by RefSeq, May 2022]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.22968858).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TSC1NM_000368.5 linkc.2836A>G p.Ser946Gly missense_variant 22/23 ENST00000298552.9 NP_000359.1 Q92574-1Q86WV8X5D9D2

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TSC1ENST00000298552.9 linkc.2836A>G p.Ser946Gly missense_variant 22/231 NM_000368.5 ENSP00000298552.3 Q92574-1
TSC1ENST00000490179.4 linkc.2836A>G p.Ser946Gly missense_variant 23/243 ENSP00000495533.2 A0A2R8Y6S8

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
33
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Tuberous sclerosis 1 Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpApr 14, 2023In 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. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt TSC1 protein function. ClinVar contains an entry for this variant (Variation ID: 1355005). This variant has not been reported in the literature in individuals affected with TSC1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces serine, which is neutral and polar, with glycine, which is neutral and non-polar, at codon 946 of the TSC1 protein (p.Ser946Gly). -
Hereditary cancer-predisposing syndrome Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsJan 10, 2022The p.S946G variant (also known as c.2836A>G), located in coding exon 20 of the TSC1 gene, results from an A to G substitution at nucleotide position 2836. The serine at codon 946 is replaced by glycine, an amino acid with similar properties. This amino acid position is conserved. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.082
BayesDel_addAF
Uncertain
0.022
T
BayesDel_noAF
Benign
-0.21
CADD
Benign
19
DANN
Uncertain
0.99
DEOGEN2
Uncertain
0.50
D;.;D;.;.;D;.;D;.;.;.
Eigen
Benign
0.066
Eigen_PC
Benign
0.17
FATHMM_MKL
Uncertain
0.97
D
LIST_S2
Benign
0.85
.;T;D;T;D;.;.;.;T;D;.
M_CAP
Benign
0.064
D
MetaRNN
Benign
0.23
T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Uncertain
-0.28
T
MutationAssessor
Uncertain
2.4
M;.;M;.;.;M;.;M;.;.;.
PrimateAI
Benign
0.47
T
PROVEAN
Uncertain
-2.4
N;N;N;.;.;.;.;.;.;.;.
REVEL
Uncertain
0.31
Sift
Uncertain
0.017
D;D;D;.;.;.;.;.;.;.;.
Sift4G
Uncertain
0.016
D;D;D;.;.;.;.;.;.;.;.
Polyphen
0.17
B;.;B;.;.;B;.;B;.;.;.
Vest4
0.21
MutPred
0.17
Loss of phosphorylation at S946 (P = 0.029);.;Loss of phosphorylation at S946 (P = 0.029);.;.;Loss of phosphorylation at S946 (P = 0.029);.;Loss of phosphorylation at S946 (P = 0.029);.;.;.;
MVP
0.83
MPC
0.46
ClinPred
0.94
D
GERP RS
4.5
Varity_R
0.56
gMVP
0.13

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr9-135772710; API