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NM_000548.5(TSC2):c.4225C>T (p.Arg1409Trp) AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Mar 30, 2021
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:
RCV000768352.3

Allele description [Variation Report for NM_000548.5(TSC2):c.4225C>T (p.Arg1409Trp)]

NM_000548.5(TSC2):c.4225C>T (p.Arg1409Trp)

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.4225C>T (p.Arg1409Trp)
HGVS:
  • NC_000016.10:g.2084447C>T
  • NG_005895.1:g.40142C>T
  • NM_000548.5:c.4225C>TMANE SELECT
  • NM_001077183.3:c.4024C>T
  • NM_001114382.3:c.4156C>T
  • NM_001318827.2:c.3916C>T
  • NM_001318829.2:c.3880C>T
  • NM_001318831.2:c.3493C>T
  • NM_001318832.2:c.4057C>T
  • NM_001363528.2:c.4027C>T
  • NM_001370404.1:c.4093C>T
  • NM_001370405.1:c.4096C>T
  • NM_021055.3:c.4096C>T
  • NP_000539.2:p.Arg1409Trp
  • NP_001070651.1:p.Arg1342Trp
  • NP_001107854.1:p.Arg1386Trp
  • NP_001305756.1:p.Arg1306Trp
  • NP_001305758.1:p.Arg1294Trp
  • NP_001305760.1:p.Arg1165Trp
  • NP_001305761.1:p.Arg1353Trp
  • NP_001350457.1:p.Arg1343Trp
  • NP_001357333.1:p.Arg1365Trp
  • NP_001357334.1:p.Arg1366Trp
  • NP_066399.2:p.Arg1366Trp
  • LRG_487t1:c.4225C>T
  • LRG_487:g.40142C>T
  • NC_000016.9:g.2134448C>T
  • NM_000548.3:c.4225C>T
  • NM_000548.4:c.4225C>T
  • p.(Arg1409Trp)
Protein change:
R1165W
Links:
Tuberous sclerosis database (TSC2): TSC2_00506; dbSNP: rs45517333
NCBI 1000 Genomes Browser:
rs45517333
Molecular consequence:
  • NM_000548.5:c.4225C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001077183.3:c.4024C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001114382.3:c.4156C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001318827.2:c.3916C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001318829.2:c.3880C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001318831.2:c.3493C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001318832.2:c.4057C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001363528.2:c.4027C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001370404.1:c.4093C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001370405.1:c.4096C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_021055.3:c.4096C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Lymphangiomyomatosis (LAM)
Synonyms:
Lymphangioleiomyomatosis; Lymphangioleiomyomatosis, somatic
Identifiers:
MONDO: MONDO:0011705; MedGen: C0751674; Orphanet: 538; OMIM: 606690
Name:
Isolated focal cortical dysplasia type II (FCORD2)
Synonyms:
Focal cortical dysplasia of Taylor; Cortical dysplasia of Taylor; Focal cortical dysplasia type 2; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0011818; MedGen: C1846385; OMIM: 607341; Human Phenotype Ontology: HP:0032051
Name:
Tuberous sclerosis 2 (TSC2)
Identifiers:
MONDO: MONDO:0013199; MedGen: C1860707; Orphanet: 805; OMIM: 613254

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000899058Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Mar 30, 2021) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot 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 Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago, SCV000899058.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

TSC2 NM_000548 exon 34 p.Arg1409Trp (c.4225C>T): This variant has not been reported in the literature but is present in 11/121418 European alleles in the Genome Aggregation Database (http://gnomad.broadinstitute.org/rs45517333). This variant is present in ClinVar, with several labs classifying this variant as likely benign or benign (Variation ID: 41740). Evolutionary conservation and computational predictive tools for this variant are unclear. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain.

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

Last Updated: Apr 15, 2024