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NM_004387.4(NKX2-5):c.743A>G (p.Tyr248Cys) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 8, 2017
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:
RCV000494374.1

Allele description [Variation Report for NM_004387.4(NKX2-5):c.743A>G (p.Tyr248Cys)]

NM_004387.4(NKX2-5):c.743A>G (p.Tyr248Cys)

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.743A>G (p.Tyr248Cys)
HGVS:
  • NC_000005.10:g.173232801T>C
  • NG_013340.1:g.7512A>G
  • NM_001166175.2:c.*696A>G
  • NM_001166176.2:c.*542A>G
  • NM_004387.4:c.743A>GMANE SELECT
  • NP_004378.1:p.Tyr248Cys
  • LRG_671t1:c.743A>G
  • LRG_671:g.7512A>G
  • LRG_671p1:p.Tyr248Cys
  • NC_000005.9:g.172659804T>C
  • NM_004387.3:c.743A>G
Protein change:
Y248C
Links:
dbSNP: rs1131691343
NCBI 1000 Genomes Browser:
rs1131691343
Molecular consequence:
  • NM_001166175.2:c.*696A>G - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_001166176.2:c.*542A>G - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_004387.4:c.743A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000581915GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(May 8, 2017) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000581915.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

A variant of uncertain significance has been identified in the NKX2-5 gene. The Y248C variant has not been published as pathogenic or been reported as benign to our knowledge. This variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The Y248C variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. Additionally, this substitution occurs at a position that is conserved across species. Furthermore, in silico analysis predicts this variant is probably damaging to the protein structure/function. Nevertheless, the Y248C variant lacks observation in a significant number of affected individuals, segregation data, and functional evidence, which would further clarify its pathogenicity.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024