rs760233114

chr9-132911462-T-Achr9-132911462-T-Cchr9-132911462-T-G

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2 PP2 BP4

The NM_000368.5(TSC1):c.1020A>T(p.Glu340Asp) 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. E340E) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 31)
• Consequence: TSC1 NM_000368.5 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.64

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP2: Missense variant where missense usually causes diseases, TSC1
• BP4: Computational evidence support a benign effect (MetaRNN=0.3240333).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TSC1	NM_000368.5	c.1020A>T	p.Glu340Asp	missense_variant	10/23	ENST00000298552.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TSC1	ENST00000298552.9	c.1020A>T	p.Glu340Asp	missense_variant	10/23	1	NM_000368.5	P4

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.090
BayesDel_addAF	Pathogenic	0.24	D
BayesDel_noAF	Uncertain	0.10
Cadd	Benign	17
Dann	Uncertain	0.99
DEOGEN2	Uncertain	0.43	T;.;T;.;T;.;T;.;.;.;.;.;.;.;.;.;.;T
Eigen	Benign	-0.14
Eigen_PC	Benign	-0.013
FATHMM_MKL	Uncertain	0.92	D
M_CAP	Uncertain	0.19	D
MetaRNN	Benign	0.32	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM	Uncertain	0.49	D
MutationAssessor	Benign	1.9	M;.;M;.;M;.;M;.;.;.;.;.;.;.;.;.;.;.
MutationTaster	Benign	1.0	D;N;N;N;N
PrimateAI	Benign	0.39	T
PROVEAN	Benign	-0.42	N;N;N;.;.;.;.;.;.;.;.;.;.;.;.;.;.;N
REVEL	Uncertain	0.58
Sift	Benign	0.21	T;T;T;.;.;.;.;.;.;.;.;.;.;.;.;.;.;D
Sift4G	Benign	0.42	T;T;T;.;.;.;.;.;.;.;.;.;.;.;.;.;.;T
Polyphen		0.0	B;.;B;.;B;.;B;.;.;.;.;B;B;B;.;.;.;B
Vest4		0.45
MutPred		0.51		Loss of glycosylation at T339 (P = 0.1993);.;Loss of glycosylation at T339 (P = 0.1993);Loss of glycosylation at T339 (P = 0.1993);Loss of glycosylation at T339 (P = 0.1993);Loss of glycosylation at T339 (P = 0.1993);Loss of glycosylation at T339 (P = 0.1993);Loss of glycosylation at T339 (P = 0.1993);Loss of glycosylation at T339 (P = 0.1993);.;.;Loss of glycosylation at T339 (P = 0.1993);Loss of glycosylation at T339 (P = 0.1993);Loss of glycosylation at T339 (P = 0.1993);Loss of glycosylation at T339 (P = 0.1993);Loss of glycosylation at T339 (P = 0.1993);.;Loss of glycosylation at T339 (P = 0.1993);
MVP		0.95
MPC		0.45
ClinPred		0.50	D
GERP RS		5.0
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.053
gMVP		0.19

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: chr9-135786849;