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NM_003242.6(TGFBR2):c.1062C>T (p.Leu354=) AND not specified

Germline classification:
Benign/Likely benign (5 submissions)
Last evaluated:
Aug 26, 2016
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:
RCV000125488.30

Allele description [Variation Report for NM_003242.6(TGFBR2):c.1062C>T (p.Leu354=)]

NM_003242.6(TGFBR2):c.1062C>T (p.Leu354=)

Gene:
TGFBR2:transforming growth factor beta receptor 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3p24.1
Genomic location:
Preferred name:
NM_003242.6(TGFBR2):c.1062C>T (p.Leu354=)
Other names:
p.L354L:CTC>CTT
HGVS:
  • NC_000003.12:g.30672245C>T
  • NG_007490.1:g.70744C>T
  • NM_001024847.3:c.1137C>T
  • NM_001407126.1:c.1245C>T
  • NM_001407127.1:c.1170C>T
  • NM_001407128.1:c.1089C>T
  • NM_001407129.1:c.1065C>T
  • NM_001407130.1:c.1062C>T
  • NM_001407132.1:c.957C>T
  • NM_001407133.1:c.957C>T
  • NM_001407134.1:c.957C>T
  • NM_001407135.1:c.957C>T
  • NM_001407136.1:c.957C>T
  • NM_001407137.1:c.777C>T
  • NM_001407138.1:c.702C>T
  • NM_001407139.1:c.530-16142C>T
  • NM_003242.6:c.1062C>TMANE SELECT
  • NP_001020018.1:p.Leu379=
  • NP_001020018.1:p.Leu379=
  • NP_001394055.1:p.Leu415=
  • NP_001394056.1:p.Leu390=
  • NP_001394057.1:p.Leu363=
  • NP_001394058.1:p.Leu355=
  • NP_001394059.1:p.Leu354=
  • NP_001394061.1:p.Leu319=
  • NP_001394062.1:p.Leu319=
  • NP_001394063.1:p.Leu319=
  • NP_001394064.1:p.Leu319=
  • NP_001394065.1:p.Leu319=
  • NP_001394066.1:p.Leu259=
  • NP_001394067.1:p.Leu234=
  • NP_003233.4:p.Leu354=
  • LRG_779t1:c.1137C>T
  • LRG_779t2:c.1062C>T
  • LRG_779:g.70744C>T
  • LRG_779p1:p.Leu379=
  • LRG_779p2:p.Leu354=
  • NC_000003.11:g.30713737C>T
  • NM_001024847.2:c.1137C>T
  • NM_003242.5:c.1062C>T
  • p.Leu354Leu
Links:
dbSNP: rs113194608
NCBI 1000 Genomes Browser:
rs113194608
Molecular consequence:
  • NM_001407139.1:c.530-16142C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001024847.3:c.1137C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001407126.1:c.1245C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001407127.1:c.1170C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001407128.1:c.1089C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001407129.1:c.1065C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001407130.1:c.1062C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001407132.1:c.957C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001407133.1:c.957C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001407134.1:c.957C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001407135.1:c.957C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001407136.1:c.957C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001407137.1:c.777C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001407138.1:c.702C>T - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_003242.6:c.1062C>T - synonymous variant - [Sequence Ontology: SO:0001819]
Observations:
4

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000168940GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))
Benign
(Oct 25, 2012)
germlineclinical testing

Citation Link,

SCV000272926Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
no assertion criteria provided
Benign
(Jun 4, 2015)
germlineclinical testing

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

SCV000309514PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely benigngermlineclinical testing

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

SCV000597486Genetic Services Laboratory, University of Chicago
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely benign
(Aug 26, 2016)
germlineclinical testing

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

SCV001807514Genome Diagnostics Laboratory, Amsterdam University Medical Center - VKGL Data-share Consensus
no assertion criteria provided
Benigngermlineclinical testing

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenonot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot provided54not providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

TGFBR1 and TGFBR2 mutations in patients with features of Marfan syndrome and Loeys-Dietz syndrome.

Singh KK, Rommel K, Mishra A, Karck M, Haverich A, Schmidtke J, Arslan-Kirchner M.

Hum Mutat. 2006 Aug;27(8):770-7.

PubMed [citation]
PMID:
16799921

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, SCV000168940.12

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

Description

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.

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

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000272926.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided5not providednot providedclinical testing PubMed (1)

Description

p.Leu354Leu in exon 4 of TGFBR2: This variant is not expected to have clinical s ignificance because it does not alter an amino acid residue and is not located w ithin the splice consensus sequence. It has been identified in 1.6% (236/14206) of South Asian chromosomes including 5 homozygotes by the Exome Aggregation Cons ortium (ExAC, http://exac.broadinstitute.org/; dbSNP rs113194608).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot provided5not provided4not provided

From PreventionGenetics, part of Exact Sciences, SCV000309514.1

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

From Genetic Services Laboratory, University of Chicago, SCV000597486.1

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

From Genome Diagnostics Laboratory, Amsterdam University Medical Center - VKGL Data-share Consensus, SCV001807514.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 3, 2024