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NM_000238.4(KCNH2):c.1883del (p.Gly628fs) AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jul 7, 2015
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:
RCV000478962.3

Allele description [Variation Report for NM_000238.4(KCNH2):c.1883del (p.Gly628fs)]

NM_000238.4(KCNH2):c.1883del (p.Gly628fs)

Gene:
KCNH2:potassium voltage-gated channel subfamily H member 2 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
7q36.1
Genomic location:
Preferred name:
NM_000238.4(KCNH2):c.1883del (p.Gly628fs)
HGVS:
  • NC_000007.14:g.150951511del
  • NG_008916.1:g.31417del
  • NM_000238.4:c.1883delMANE SELECT
  • NM_001204798.2:c.863del
  • NM_001406753.1:c.1594delG
  • NM_001406755.1:c.1705delG
  • NM_001406756.1:c.1594delG
  • NM_001406757.1:c.1582delG
  • NM_172056.3:c.1882delG
  • NM_172057.3:c.863del
  • NP_000229.1:p.Gly628Alafs
  • NP_000229.1:p.Gly628fs
  • NP_001191727.1:p.Gly288fs
  • NP_001393682.1:p.Gly532Alafs
  • NP_001393684.1:p.Gly569Alafs
  • NP_001393685.1:p.Gly532Alafs
  • NP_001393686.1:p.Gly528Alafs
  • NP_742053.1:p.Gly628Alafs
  • NP_742053.1:p.Gly628fs
  • NP_742054.1:p.Gly288Alafs
  • NP_742054.1:p.Gly288fs
  • LRG_288t1:c.1882del
  • LRG_288t2:c.1883del
  • LRG_288t3:c.862del
  • LRG_288:g.31417del
  • LRG_288p1:p.Gly628Alafs
  • LRG_288p2:p.Gly628fs
  • LRG_288p3:p.Gly288Alafs
  • NC_000007.13:g.150648599del
  • NM_000238.2:c.1883delG
  • NM_000238.3:c.1882delG
  • NM_172056.2:c.1883del
  • NM_172057.2:c.862delG
  • NR_176254.1:n.2290delG
  • NR_176255.1:n.1163delG
Protein change:
G288fs
Links:
dbSNP: rs1064793855
NCBI 1000 Genomes Browser:
rs1064793855
Molecular consequence:
  • NM_000238.4:c.1883del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001204798.2:c.863del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406753.1:c.1594delG - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406755.1:c.1705delG - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406756.1:c.1594delG - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001406757.1:c.1582delG - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_172056.3:c.1882delG - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_172057.3:c.863del - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: CN517202

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000567187GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Pathogenic
(Jul 7, 2015) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000567187.3

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

Description

Although the c.1883delG deletion in the KCNH2 gene has not been reported to our knowledge, thisvariant causes a shift in reading frame starting at codon Glycine 628, changing it to an Alanine, andcreating a premature stop codon at position 86 of the new reading frame, denoted p.Gly628AlafsX86. Thisdeletion is expected to result in either an abnormal, truncated protein product or loss of protein from thisallele through nonsense-mediated mRNA decay. Other frameshift variants in the KCNH2 gene havebeen reported in HGMD in association with LQTS (Stenson P et al., 2014). Furthermore, the c.1883delGvariant was not observed in approximately 6,500 individuals of European and African American ancestryin the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations.In summary, c.1883delG in the KCNH2 gene is interpreted as a pathogenic variant.

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

Last Updated: Nov 5, 2022