NM_003239.5(TGFB3):c.859C>T (p.Arg287Trp) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Feb 28, 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:: RCV000756774.17

Allele description [Variation Report for NM_003239.5(TGFB3):c.859C>T (p.Arg287Trp)]

NM_003239.5(TGFB3):c.859C>T (p.Arg287Trp)

Gene:

TGFB3:transforming growth factor beta 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

14q24.3

Genomic location:

Preferred name:

NM_003239.5(TGFB3):c.859C>T (p.Arg287Trp)

HGVS:

NC_000014.9:g.75963383G>A
NG_011715.1:g.23367C>T
NM_001329938.2:c.859C>T
NM_001329939.2:c.859C>T
NM_003239.5:c.859C>TMANE SELECT
NP_001316867.1:p.Arg287Trp
NP_001316868.1:p.Arg287Trp
NP_003230.1:p.Arg287Trp
NP_003230.1:p.Arg287Trp
LRG_399t1:c.859C>T
LRG_399:g.23367C>T
NC_000014.8:g.76429726G>A
NM_003239.2:c.859C>T
NM_003239.3:c.859C>T
NM_003239.4:c.859C>T
NM_003239.5:c.859C>T

Protein change:

R287W

Links:

dbSNP: rs757774610

NCBI 1000 Genomes Browser:

rs757774610

Molecular consequence:

NM_001329938.2:c.859C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001329939.2:c.859C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_003239.5:c.859C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000884684	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process)	Uncertain significance (Mar 21, 2018)	germline	clinical testing	Citation Link,
SCV003918210	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Feb 28, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000884684

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process)

Uncertain significance
(Mar 21, 2018)

germline

clinical testing

Citation Link,

SCV003918210

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Feb 28, 2023)

germline

clinical testing

Citation Link

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV000884684.1

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

Description

The TGFB3: p.Arg287Trp variant (rs757774610) has not been reported in the medical literature, gene specific variation databases, nor has it been previously identified by our laboratory. This variant is listed in the Genome Aggregation Database (gnomAD) with a frequency of 0.02 percent in the Latino population (identified on 8 out of 34,418 chromosomes). The arginine at position 287 is highly conserved up to zebrafish considering 12 species (Alamut v2.10) and computational analyses of the p.Arg287Trp variant on protein structure and function indicate a deleterious effect (SIFT: damaging, PolyPhen-2: probably damaging). Altogether, there is not enough evidence to classify the p.Arg287Trp variant with certainty.

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

From GeneDx, SCV003918210.1

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

Description

Has not been previously published as pathogenic or benign to our knowledge; In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 26582918)

#	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

Last Updated: Nov 10, 2024

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