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NM_000548.5(TSC2):c.3333G>A (p.Lys1111=) AND Tuberous sclerosis syndrome

Germline classification:
Benign/Likely benign (2 submissions)
Last evaluated:
Feb 5, 2024
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:
RCV000344533.7

Allele description [Variation Report for NM_000548.5(TSC2):c.3333G>A (p.Lys1111=)]

NM_000548.5(TSC2):c.3333G>A (p.Lys1111=)

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.3333G>A (p.Lys1111=)
Other names:
p.K1111K:AAG>AAA
HGVS:
  • NC_000016.10:g.2079605G>A
  • NG_005895.1:g.35300G>A
  • NM_000548.5:c.3333G>AMANE SELECT
  • NM_001077183.3:c.3201G>A
  • NM_001114382.3:c.3333G>A
  • NM_001318827.2:c.3093G>A
  • NM_001318829.2:c.3057G>A
  • NM_001318831.2:c.2601G>A
  • NM_001318832.2:c.3234G>A
  • NM_001363528.2:c.3204G>A
  • NM_001370404.1:c.3201G>A
  • NM_001370405.1:c.3204G>A
  • NM_021055.3:c.3204G>A
  • NP_000539.2:p.Lys1111=
  • NP_001070651.1:p.Lys1067=
  • NP_001107854.1:p.Lys1111=
  • NP_001305756.1:p.Lys1031=
  • NP_001305758.1:p.Lys1019=
  • NP_001305760.1:p.Lys867=
  • NP_001305761.1:p.Lys1078=
  • NP_001350457.1:p.Lys1068=
  • NP_001357333.1:p.Lys1067=
  • NP_001357334.1:p.Lys1068=
  • NP_066399.2:p.Lys1068=
  • LRG_487t1:c.3333G>A
  • LRG_487:g.35300G>A
  • NC_000016.9:g.2129606G>A
  • NM_000548.3:c.3333G>A
  • NM_000548.4:c.3333G>A
Links:
dbSNP: rs557648435
NCBI 1000 Genomes Browser:
rs557648435
Molecular consequence:
  • NM_000548.5:c.3333G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001077183.3:c.3201G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001114382.3:c.3333G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001318827.2:c.3093G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001318829.2:c.3057G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001318831.2:c.2601G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001318832.2:c.3234G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001363528.2:c.3204G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001370404.1:c.3201G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001370405.1:c.3204G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_021055.3:c.3204G>A - synonymous variant - [Sequence Ontology: SO:0001819]
Observations:
20

Condition(s)

Name:
Tuberous sclerosis syndrome (TSC)
Synonyms:
Tuberous sclerosis
Identifiers:
MONDO: MONDO:0001734; MedGen: C0041341; OMIM: PS191100

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000395625Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSL Variant Classification Criteria 13 December 2019)		Likely benign
(Apr 27, 2017) 		germlineclinical testing

Citation Link,

SCV004817477All of Us Research Program, National Institutes of Health
criteria provided, single submitter

(ACMG Guidelines, 2015)		Benign
(Feb 5, 2024) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown20not providednot provided108544not providedclinical 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 Illumina Laboratory Services, Illumina, SCV000395625.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From All of Us Research Program, National Institutes of Health, SCV004817477.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided20not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknown108544not providednot provided20not providednot providednot provided

Last Updated: May 25, 2025