NM_003239.5(TGFB3):c.757G>A (p.Val253Met) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Jul 18, 2022
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:: RCV001592863.17

Allele description [Variation Report for NM_003239.5(TGFB3):c.757G>A (p.Val253Met)]

NM_003239.5(TGFB3):c.757G>A (p.Val253Met)

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.757G>A (p.Val253Met)

HGVS:

NC_000014.9:g.75963485C>T
NG_011715.1:g.23265G>A
NM_001329938.2:c.757G>A
NM_001329939.2:c.757G>A
NM_003239.5:c.757G>AMANE SELECT
NP_001316867.1:p.Val253Met
NP_001316868.1:p.Val253Met
NP_003230.1:p.Val253Met
LRG_399t1:c.757G>A
LRG_399:g.23265G>A
NC_000014.8:g.76429828C>T
NM_003239.2:c.757G>A
NM_003239.3:c.757G>A

Protein change:

V253M

Links:

dbSNP: rs532517095

NCBI 1000 Genomes Browser:

rs532517095

Molecular consequence:

NM_001329938.2:c.757G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001329939.2:c.757G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_003239.5:c.757G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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PREDICTED: Rattus norvegicus protein kinase cAMP-dependent type I regulatory sub...
PREDICTED: Rattus norvegicus protein kinase cAMP-dependent type I regulatory subunit beta (Prkar1b), transcript variant X4, mRNA
gi|2678887168|ref|XM_039089118.2|

Nucleotide
Rattus norvegicus TL0AEA68YK14 mRNA sequence
Rattus norvegicus TL0AEA68YK14 mRNA sequence
gi|298902200|emb|FQ231663.1|

Nucleotide
Homo sapiens 211000035836695 genomic scaffold, whole genome shotgun sequence
Homo sapiens 211000035836695 genomic scaffold, whole genome shotgun sequence
gi|71518097|gb|CH471061.1||gnl|WGS: 211000035836695

Nucleotide
Homo sapiens transforming growth factor, beta 3 (TGFB3) gene, complete cds
Homo sapiens transforming growth factor, beta 3 (TGFB3) gene, complete cds
gi|27501939|gb|AY208161.1|

Nucleotide
Eno1l1 enolase 1 like 1 [Rattus norvegicus]
Eno1l1 enolase 1 like 1 [Rattus norvegicus]
Gene ID:108351291

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001471877	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process)	Uncertain significance (Mar 18, 2020)	germline	clinical testing	Citation Link,
SCV001823222	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Jul 18, 2022)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001471877

ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

criteria provided, single submitter

(ARUP Molecular Germline Variant Investigation Process)

Uncertain significance
(Mar 18, 2020)

germline

clinical testing

Citation Link,

SCV001823222

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Jul 18, 2022)

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	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, SCV001471877.1

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

Description

The TGFB3 c.757G>A; p.Val253Met variant (rs532517095), to our knowledge, is not reported in the medical literature but is reported in ClinVar (Variation ID: 566598). This variant is found in the African population with an overall allele frequency of 0.03% (8/24966 alleles) in the Genome Aggregation Database. The valine at codon 253 is moderately conserved, and computational analyses (SIFT, PolyPhen-2) predict that this variant is tolerated. However, due to limited information, the clinical significance of the p.Val253Met variant is uncertain at this time.

#	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, SCV001823222.3

#	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 does not alter protein structure/function

#	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: Aug 25, 2024

ClinVar

Relating variation to medicine