NM_004387.4(NKX2-5):c.865AAC[2] (p.Asn291del) AND Cardiovascular phenotype

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 10, 2021
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:: RCV002374804.2

Allele description [Variation Report for NM_004387.4(NKX2-5):c.865AAC[2] (p.Asn291del)]

NM_004387.4(NKX2-5):c.865AAC[2] (p.Asn291del)

Gene:

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

Variant type:

Microsatellite

Cytogenetic location:

5q35.1

Genomic location:

Preferred name:

NM_004387.4(NKX2-5):c.865AAC[2] (p.Asn291del)

HGVS:

NC_000005.10:g.173232672TTG[2]
NG_013340.1:g.7634AAC[2]
NM_001166175.2:c.*818AAC[2]
NM_001166176.2:c.*664AAC[2]
NM_004387.4:c.865AAC[2]MANE SELECT
NP_004378.1:p.Asn291del
LRG_671t1:c.865AAC[2]
LRG_671:g.7634AAC[2]
LRG_671p1:p.Asn291del
NC_000005.9:g.172659674_172659676del
NC_000005.9:g.172659675TTG[2]
NM_004387.3:c.871_873del
NM_004387.3:c.871_873delAAC
NM_004387.4:c.871_873delMANE SELECT

Protein change:

N291del

Links:

OMIM: 600584.0020; dbSNP: rs756974215

NCBI 1000 Genomes Browser:

rs756974215

Molecular consequence:

NM_001166175.2:c.*818AAC[2] - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001166176.2:c.*664AAC[2] - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_004387.4:c.865AAC[2] - inframe_deletion - [Sequence Ontology: SO:0001822]

Condition(s)

Name:: Cardiovascular phenotype
Identifiers:: MedGen: CN230736

Recent activity

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MULTISPECIES: DgaE family pyridoxal phosphate-dependent ammonia lyase [unclassif...
MULTISPECIES: DgaE family pyridoxal phosphate-dependent ammonia lyase [unclassified Citrobacter]
gi|1883368059|ref|WP_181221140.1|

Protein
MULTISPECIES: trehalose operon repressor TreR [unclassified Citrobacter]
MULTISPECIES: trehalose operon repressor TreR [unclassified Citrobacter]
gi|1883368073|ref|WP_181221154.1|

Protein
MULTISPECIES: KDGP aldolase family protein [unclassified Citrobacter]
MULTISPECIES: KDGP aldolase family protein [unclassified Citrobacter]
gi|1883368060|ref|WP_181221141.1|

Protein
Phenacobius teretulus voucher UTEIC 44.11724 ryanodine receptor 3-like protein (...
Phenacobius teretulus voucher UTEIC 44.11724 ryanodine receptor 3-like protein (RYR3) gene, partial cds
gi|336051522|gb|JF949816.1|

Nucleotide
snt-5 C2 domain-containing protein [Caenorhabditis elegans]
snt-5 C2 domain-containing protein [Caenorhabditis elegans]
Gene ID:178631

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002684160	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Uncertain significance (May 10, 2021)	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

SCV002684160

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Uncertain significance
(May 10, 2021)

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

NKX2.5 mutations in patients with congenital heart disease.

McElhinney DB, Geiger E, Blinder J, Benson DW, Goldmuntz E.

J Am Coll Cardiol. 2003 Nov 5;42(9):1650-5.

PubMed [citation]

PMID:: 14607454

Details of each submission

From Ambry Genetics, SCV002684160.2

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

Description

The c.871_873delAAC variant (also known as p.N291del) is located in coding exon 2 of the NKX2-5 gene. This variant results from an in-frame AAC deletion at nucleotide positions 871 to 873. This results in the in-frame deletion of an asparagine at codon 291. This variant was reported in one individual from a congenital heart defect cohort, as well as in an unaffected parent (McElhinney DB et al. J Am Coll Cardiol, 2003 Nov;42:1650-5). This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be neutral by in silico analysis (Choi Y et al., PLoS ONE 2012; 7(10):e46688). 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: Sep 29, 2024

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