NM_000548.5(TSC2):c.3145G>A (p.Glu1049Lys) AND not provided

Germline classification:: Uncertain significance (3 submissions)
Last evaluated:: Nov 6, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000766975.14

Allele description [Variation Report for NM_000548.5(TSC2):c.3145G>A (p.Glu1049Lys)]

NM_000548.5(TSC2):c.3145G>A (p.Glu1049Lys)

Gene:

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

Variant type:

single nucleotide variant

Cytogenetic location:

16p13.3

Genomic location:

Preferred name:

NM_000548.5(TSC2):c.3145G>A (p.Glu1049Lys)

Other names:

p.E1049K:GAG>AAG

HGVS:

NC_000016.10:g.2079289G>A
NG_005895.1:g.34984G>A
NM_000548.5:c.3145G>AMANE SELECT
NM_001077183.3:c.3013G>A
NM_001114382.3:c.3145G>A
NM_001318827.2:c.2905G>A
NM_001318829.2:c.2869G>A
NM_001318831.2:c.2413G>A
NM_001318832.2:c.3046G>A
NM_001363528.2:c.3016G>A
NM_001370404.1:c.3013G>A
NM_001370405.1:c.3016G>A
NM_021055.3:c.3016G>A
NP_000539.2:p.Glu1049Lys
NP_001070651.1:p.Glu1005Lys
NP_001107854.1:p.Glu1049Lys
NP_001305756.1:p.Glu969Lys
NP_001305758.1:p.Glu957Lys
NP_001305760.1:p.Glu805Lys
NP_001305761.1:p.Glu1016Lys
NP_001350457.1:p.Glu1006Lys
NP_001357333.1:p.Glu1005Lys
NP_001357334.1:p.Glu1006Lys
NP_066399.2:p.Glu1006Lys
LRG_487t1:c.3145G>A
LRG_487:g.34984G>A
NC_000016.9:g.2129290G>A
NM_000548.3:c.3145G>A
NM_000548.4:c.3145G>A
NM_001077183.1:c.3013G>A

Protein change:

E1005K

Links:

dbSNP: rs796053492

NCBI 1000 Genomes Browser:

rs796053492

Molecular consequence:

NM_000548.5:c.3145G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001077183.3:c.3013G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001114382.3:c.3145G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001318827.2:c.2905G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001318829.2:c.2869G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001318831.2:c.2413G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001318832.2:c.3046G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001363528.2:c.3016G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370404.1:c.3013G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001370405.1:c.3016G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_021055.3:c.3016G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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uncharacterized protein LOC101217980 isoform X3 [Cucumis sativus]
uncharacterized protein LOC101217980 isoform X3 [Cucumis sativus]
gi|778718350|ref|XP_011657854.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000243686	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Nov 6, 2023)	germline	clinical testing	Citation Link,
SCV000920701	Gharavi Laboratory, Columbia University	no assertion criteria provided (ACMG Guidelines, 2015)	Uncertain significance (Sep 16, 2018)	germline	research	PubMed (1) [See all records that cite this PMID]
SCV002011338	Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Nov 3, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000243686

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Nov 6, 2023)

germline

clinical testing

Citation Link,

SCV000920701

Gharavi Laboratory, Columbia University

no assertion criteria provided

(ACMG Guidelines, 2015)

Uncertain significance
(Sep 16, 2018)

germline

research

PubMed (1)
[See all records that cite this PMID]

SCV002011338

Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Nov 3, 2021)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

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
not provided	germline	no	not provided	not provided	not provided	not provided	not provided	research
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From GeneDx, SCV000243686.15

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

Description

In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Observed in a patient with cardiac rhabdomyoma; however, no other features of TSC were noted in the patient (PMID: 19254590); This variant is associated with the following publications: (PMID: 22558107, 34426522, 37800821, 19254590)

#	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

From Gharavi Laboratory, Columbia University, SCV000920701.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	research	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	no	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden, SCV002011338.3

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

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

Last Updated: Sep 16, 2024

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