NM_003242.6(TGFBR2):c.776A>G (p.Tyr259Cys) AND Loeys-Dietz syndrome 2

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Apr 3, 2023
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:: RCV004006693.2

Allele description [Variation Report for NM_003242.6(TGFBR2):c.776A>G (p.Tyr259Cys)]

NM_003242.6(TGFBR2):c.776A>G (p.Tyr259Cys)

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.776A>G (p.Tyr259Cys)

HGVS:

NC_000003.12:g.30671959A>G
NG_007490.1:g.70458A>G
NM_001024847.3:c.851A>G
NM_001407126.1:c.959A>G
NM_001407127.1:c.884A>G
NM_001407128.1:c.803A>G
NM_001407129.1:c.779A>G
NM_001407130.1:c.776A>G
NM_001407132.1:c.671A>G
NM_001407133.1:c.671A>G
NM_001407134.1:c.671A>G
NM_001407135.1:c.671A>G
NM_001407136.1:c.671A>G
NM_001407137.1:c.491A>G
NM_001407138.1:c.416A>G
NM_003242.6:c.776A>GMANE SELECT
NP_001020018.1:p.Tyr284Cys
NP_001020018.1:p.Tyr284Cys
NP_001394055.1:p.Tyr320Cys
NP_001394056.1:p.Tyr295Cys
NP_001394057.1:p.Tyr268Cys
NP_001394058.1:p.Tyr260Cys
NP_001394059.1:p.Tyr259Cys
NP_001394061.1:p.Tyr224Cys
NP_001394062.1:p.Tyr224Cys
NP_001394063.1:p.Tyr224Cys
NP_001394064.1:p.Tyr224Cys
NP_001394065.1:p.Tyr224Cys
NP_001394066.1:p.Tyr164Cys
NP_001394067.1:p.Tyr139Cys
NP_003233.4:p.Tyr259Cys
LRG_779t1:c.851A>G
LRG_779t2:c.776A>G
LRG_779:g.70458A>G
LRG_779p1:p.Tyr284Cys
LRG_779p2:p.Tyr259Cys
NC_000003.11:g.30713451A>G
NC_000003.11:g.30713451A>G
NM_001024847.2:c.851A>G
NM_003242.5:c.776A>G

Protein change:

Y139C

Links:

dbSNP: rs767919854

NCBI 1000 Genomes Browser:

rs767919854

Molecular consequence:

NM_001024847.3:c.851A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407126.1:c.959A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407127.1:c.884A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407128.1:c.803A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407129.1:c.779A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407130.1:c.776A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407132.1:c.671A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407133.1:c.671A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407134.1:c.671A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407135.1:c.671A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407136.1:c.671A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407137.1:c.491A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001407138.1:c.416A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_003242.6:c.776A>G - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Name:: Loeys-Dietz syndrome 2 (LDS2)
Synonyms:: Loeys-Dietz syndrome type 1B; MARFAN SYNDROME, TYPE II; Loeys-Dietz syndrome type 2B; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0012427; MedGen: C2674574; Orphanet: 558; OMIM: 610168

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004839196	All of Us Research Program, National Institutes of Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain Significance (Apr 3, 2023)	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

SCV004839196

All of Us Research Program, National Institutes of Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain Significance
(Apr 3, 2023)

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	unknown	1	not provided	not provided	108544	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 All of Us Research Program, National Institutes of Health, SCV004839196.1

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

Description

This missense variant replaces tyrosine with cysteine at codon 259 of the TGFBR2 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). Splice site prediction tools suggest that this variant may not impact RNA splicing. To our knowledge, functional studies have not been performed for this variant. This variant has not been reported in individuals affected with cardiovascular disorders in the literature. This variant has been identified in 4/249502 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	108544	not provided	not provided		1	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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