NM_000548.5(TSC2):c.5391CTC[1] (p.Ser1799del) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 17, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000189952.7

Allele description [Variation Report for NM_000548.5(TSC2):c.5391CTC[1] (p.Ser1799del)]

NM_000548.5(TSC2):c.5391CTC[1] (p.Ser1799del)

Gene:

TSC2:TSC complex subunit 2 [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

16p13.3

Genomic location:

Preferred name:

NM_000548.5(TSC2):c.5391CTC[1] (p.Ser1799del)

HGVS:

NC_000016.10:g.2088577CTC[1]
NG_005895.1:g.44272CTC[1]
NG_008617.1:g.54639GAG[1]
NM_000548.5:c.5391CTC[1]MANE SELECT
NM_001077183.3:c.5190CTC[1]
NM_001114382.3:c.5322CTC[1]
NM_001318827.2:c.5082CTC[1]
NM_001318829.2:c.5046CTC[1]
NM_001318831.2:c.4659CTC[1]
NM_001318832.2:c.5223CTC[1]
NM_001363528.2:c.5193CTC[1]
NM_001370404.1:c.5259CTC[1]
NM_001370405.1:c.5250CTC[1]
NM_021055.3:c.5262CTC[1]
NP_000539.2:p.Ser1799del
NP_001070651.1:p.Ser1732del
NP_001107854.1:p.Ser1776del
NP_001305756.1:p.Ser1696del
NP_001305758.1:p.Ser1684del
NP_001305760.1:p.Ser1555del
NP_001305761.1:p.Ser1743del
NP_001350457.1:p.Ser1733del
NP_001357333.1:p.Ser1755del
NP_001357334.1:p.Ser1752del
NP_066399.2:p.Ser1756del
LRG_487t1:c.5394_5396del
LRG_487:g.44272CTC[1]
NC_000016.9:g.2138578CTC[1]
NC_000016.9:g.2138578_2138580del
NM_000548.3:c.5394_5396del
NM_000548.3:c.5394_5396delCTC
NM_000548.4:c.5394_5396del
p.S1799del

Protein change:

S1555del

Links:

dbSNP: rs796053480

NCBI 1000 Genomes Browser:

rs796053480

Molecular consequence:

NM_000548.5:c.5391CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001077183.3:c.5190CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001114382.3:c.5322CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001318827.2:c.5082CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001318829.2:c.5046CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001318831.2:c.4659CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001318832.2:c.5223CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001363528.2:c.5193CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001370404.1:c.5259CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_001370405.1:c.5250CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]
NM_021055.3:c.5262CTC[1] - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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PREDICTED: Homo sapiens TBC1 domain containing kinase (TBCK), transcript variant...
PREDICTED: Homo sapiens TBC1 domain containing kinase (TBCK), transcript variant X5, mRNA
gi|2462599798|ref|XM_054351274.1|

Nucleotide
TBC domain-containing protein kinase-like protein isoform X4 [Homo sapiens]
TBC domain-containing protein kinase-like protein isoform X4 [Homo sapiens]
gi|2462599807|ref|XP_054207253.1|

Protein
TBC domain-containing protein kinase-like protein isoform X2 [Homo sapiens]
TBC domain-containing protein kinase-like protein isoform X2 [Homo sapiens]
gi|2217352693|ref|XP_047272378.1|

Protein
PREDICTED: Homo sapiens ubiquinol-cytochrome c reductase complex assembly factor...
PREDICTED: Homo sapiens ubiquinol-cytochrome c reductase complex assembly factor 1 (UQCC1), transcript variant X5, mRNA
gi|2462580709|ref|XM_054323611.1|

Nucleotide
Saccharomyces cerevisiae S288C Pxp2p (PXP2), partial mRNA
Saccharomyces cerevisiae S288C Pxp2p (PXP2), partial mRNA
gi|296146116|ref|NM_001181769.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000243620	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Aug 17, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000243620

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Aug 17, 2022)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000243620.8

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

In-frame deletion of 1 amino acid in a non-repeat region; Previously reported as a variant of uncertain significance in a woman with a clinical diagnosis of tuberous sclerosis and lymphangioleiomyomatosis (Liu et al., 2019); In silico analysis supports a deleterious effect on protein structure/function; Published functional studies demonstrate reduced levels of TSC1 and TSC2 protein and elevated levels of phosphorylated AKT (Mrozek et al., 2021); This variant is associated with the following publications: (PMID: 31856217, 33891611)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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