NM_004387.4(NKX2-5):c.835T>G (p.Ser279Ala) AND Cardiovascular phenotype

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 23, 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:: RCV003172155.2

Allele description [Variation Report for NM_004387.4(NKX2-5):c.835T>G (p.Ser279Ala)]

NM_004387.4(NKX2-5):c.835T>G (p.Ser279Ala)

Gene:

NKX2-5:NK2 homeobox 5 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

5q35.1

Genomic location:

Preferred name:

NM_004387.4(NKX2-5):c.835T>G (p.Ser279Ala)

HGVS:

NC_000005.10:g.173232709A>C
NG_013340.1:g.7604T>G
NG_106657.1:g.684A>C
NM_001166175.2:c.*788T>G
NM_001166176.2:c.*634T>G
NM_004387.4:c.835T>GMANE SELECT
NP_004378.1:p.Ser279Ala
LRG_671t1:c.835T>G
LRG_671:g.7604T>G
LRG_671p1:p.Ser279Ala
NC_000005.9:g.172659712A>C
NM_004387.3:c.835T>G

Protein change:

S279A

Molecular consequence:

NM_001166175.2:c.*788T>G - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001166176.2:c.*634T>G - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_004387.4:c.835T>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Cardiovascular phenotype
Identifiers:: MedGen: CN230736

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003858938	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (Jan 23, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID] Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003858938

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(Jan 23, 2023)

germline

clinical testing

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

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

Citations

PubMed

An update on genetic variants of the NKX2-5.

Kolomenski JE, Delea M, Simonetti L, Fabbro MC, Espeche LD, Taboas M, Nadra AD, Bruque CD, Dain L.

Hum Mutat. 2020 Jul;41(7):1187-1208. doi: 10.1002/humu.24030. Epub 2020 May 22.

PubMed [citation]

PMID:: 32369864

Details of each submission

From Ambry Genetics, SCV003858938.2

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

Description

The p.S279A variant (also known as c.835T>G), located in coding exon 2 of the NKX2-5 gene, results from a T to G substitution at nucleotide position 835. The serine at codon 279 is replaced by alanine, an amino acid with similar properties. This amino acid position is poorly conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

#	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

Last Updated: May 1, 2024

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