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NM_000238.4(KCNH2):c.916G>T (p.Gly306Trp) AND not provided

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Jun 10, 2016
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:
RCV000182020.3

Allele description [Variation Report for NM_000238.4(KCNH2):c.916G>T (p.Gly306Trp)]

NM_000238.4(KCNH2):c.916G>T (p.Gly306Trp)

Gene:
KCNH2:potassium voltage-gated channel subfamily H member 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
7q36.1
Genomic location:
Preferred name:
NM_000238.4(KCNH2):c.916G>T (p.Gly306Trp)
Other names:
p.G306W:GGG>TGG
HGVS:
  • NC_000007.14:g.150958059C>A
  • NG_008916.1:g.24868G>T
  • NM_000238.4:c.916G>TMANE SELECT
  • NM_001406753.1:c.628G>T
  • NM_001406755.1:c.739G>T
  • NM_001406756.1:c.628G>T
  • NM_001406757.1:c.616G>T
  • NM_172056.3:c.916G>T
  • NP_000229.1:p.Gly306Trp
  • NP_000229.1:p.Gly306Trp
  • NP_001393682.1:p.Gly210Trp
  • NP_001393684.1:p.Gly247Trp
  • NP_001393685.1:p.Gly210Trp
  • NP_001393686.1:p.Gly206Trp
  • NP_742053.1:p.Gly306Trp
  • NP_742053.1:p.Gly306Trp
  • LRG_288t1:c.916G>T
  • LRG_288t2:c.916G>T
  • LRG_288:g.24868G>T
  • LRG_288p1:p.Gly306Trp
  • LRG_288p2:p.Gly306Trp
  • NC_000007.13:g.150655147C>A
  • NM_000238.2:c.916G>T
  • NM_000238.3:c.916G>T
  • NM_172056.2:c.916G>T
  • NR_176254.1:n.1324G>T
Protein change:
G206W
Links:
dbSNP: rs199472884
NCBI 1000 Genomes Browser:
rs199472884
Molecular consequence:
  • NM_000238.4:c.916G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406753.1:c.628G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406755.1:c.739G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406756.1:c.628G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001406757.1:c.616G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_172056.3:c.916G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000234323GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Likely pathogenic
(Jun 10, 2016) 		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, SCV000234323.7

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

Description

The G306W variant in the KCNH2 gene has been reported in at least one individual with LQTS and has not been observed in >1000 control alleles (Tester D et al., 2005; Kapa et al., 2009; Giudicessi et al., 2012). Of note, coverage of this nucleotide position in these control alleles was not reported, and presence or absence in the NHLBI Exome Sequencing Project was unable to be determined due to inadequate coverage (1X). This variant was also seen co-segregating with LQTS in four relatives referred for genetic testing at GeneDx. Additionally, G306W is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. This substitution occurs at a position that is conserved across species, and in silico analysis predicts this variant is probably damaging to the protein structure/function. The Guanine nucleotide at position c.916 is the 3'-terminal nucleotide of exon 4, and two out of three splicing algorithms suggest that this nucleotide substitution either damages or destroys the canonical splice donor site at this exon/intron junction. Other missense variants in KCNH2 that are predicted to affect splicing have been reported in the Human Genome Database (HGMD) in association with LQTS (Stenson et al., 2014). Lastly, a variant at the same residue (G306R) has also been reported in HGMD in association with LQTS. Therefore, G306W is a strong candidate to be pathogenic. Nevertheless, additional segregation and functional studies are necessary to clarify the role of this variant in disease.

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

Last Updated: Feb 20, 2024