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NM_001378969.1(KCND3):c.1119G>A (p.Met373Ile) AND Variant of unknown significance

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Dec 1, 2012
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
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:
RCV000056300.3

Allele description [Variation Report for NM_001378969.1(KCND3):c.1119G>A (p.Met373Ile)]

NM_001378969.1(KCND3):c.1119G>A (p.Met373Ile)

Gene:
KCND3:potassium voltage-gated channel subfamily D member 3 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p13.2
Genomic location:
Preferred name:
NM_001378969.1(KCND3):c.1119G>A (p.Met373Ile)
HGVS:
  • NC_000001.11:g.111787094C>T
  • NG_032011.2:g.207062G>A
  • NM_001378969.1:c.1119G>AMANE SELECT
  • NM_001378970.1:c.1119G>A
  • NM_004980.5:c.1119G>A
  • NM_172198.3:c.1119G>A
  • NP_001365898.1:p.Met373Ile
  • NP_001365899.1:p.Met373Ile
  • NP_004971.2:p.Met373Ile
  • NP_004971.2:p.Met373Ile
  • NP_751948.1:p.Met373Ile
  • LRG_445t1:c.1119G>A
  • LRG_445:g.207062G>A
  • LRG_445p1:p.Met373Ile
  • NC_000001.10:g.112329716C>T
  • NM_004980.4:c.1119G>A
  • Q9UK17:p.Met373Ile
Protein change:
M373I; MET373ILE
Links:
UniProtKB: Q9UK17#VAR_070789; OMIM: 605411.0003; dbSNP: rs397515477
NCBI 1000 Genomes Browser:
rs397515477
Molecular consequence:
  • NM_001378969.1:c.1119G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001378970.1:c.1119G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_004980.5:c.1119G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_172198.3:c.1119G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Variant of unknown significance
Identifiers:
MedGen: C2986382

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000087469OMIM
no assertion criteria provided
Uncertain significance
(Dec 1, 2012)
germlineliterature only

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Mutations in potassium channel kcnd3 cause spinocerebellar ataxia type 19.

Duarri A, Jezierska J, Fokkens M, Meijer M, Schelhaas HJ, den Dunnen WF, van Dijk F, Verschuuren-Bemelmans C, Hageman G, van de Vlies P, Küsters B, van de Warrenburg BP, Kremer B, Wijmenga C, Sinke RJ, Swertz MA, Kampinga HH, Boddeke E, Verbeek DS.

Ann Neurol. 2012 Dec;72(6):870-80. doi: 10.1002/ana.23700.

PubMed [citation]
PMID:
23280838

Details of each submission

From OMIM, SCV000087469.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (1)

Description

This variant is classified as a variant of unknown significance because its contribution to spinocerebellar ataxia-19 (607346) has not been confirmed.

In a Dutch father and daughter with late-onset spinocerebellar ataxia, Duarri et al. (2012) identified a heterozygous c.1119G-A transition in the KCND3 gene, resulting in a met373-to-ile (M373I) substitution at a highly conserved residue. The mutation was initially found by direct sequencing of the KCND3 gene in 230 Dutch probands with ataxia in whom mutations in several known SCA genes were not identified. It was not present in the dbSNP, 1000 Genomes Project, or Exome Variant Server databases, or in 800 Dutch control chromosomes. The proband had ambiguous neurologic signs on testing at age 44 years, and later had no neurologic signs at age 52 years, consistent with being an asymptomatic carrier. He had a relevant family history, with both his father and a sister showing signs of the disorder. His father was more severely affected, with onset of progressive ataxic gait at age 55 years, dysarthria, and cerebellar atrophy on brain MRI. His sister had very mild gait impairment at age 64 years. Transfection of the M373I mutation into HeLa cells showed that the mutant protein had almost no cell surface expression, but rather accumulated in the endoplasmic reticulum, consistent with a trafficking defect. The mutant protein was more rapidly degraded compared to the wildtype protein, suggesting that it was misfolded. The trafficking and degradation defects could be rescued by coexpression with the active isoform of KCHIP2 (604661). Patch-clamp recordings showed that the mutant channel had decreased current activity (25% of controls).

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

Last Updated: Sep 16, 2024