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NM_001161352.2(KCNMA1):c.16G>A (p.Gly6Ser) AND Generalized epilepsy-paroxysmal dyskinesia syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Nov 16, 2022
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:
RCV000639889.11

Allele description

NM_001161352.2(KCNMA1):c.16G>A (p.Gly6Ser)

Gene:
KCNMA1:potassium calcium-activated channel subfamily M alpha 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
10q22.3
Genomic location:
Preferred name:
NM_001161352.2(KCNMA1):c.16G>A (p.Gly6Ser)
HGVS:
  • NC_000010.11:g.77637627C>T
  • NG_012270.1:g.5193G>A
  • NM_001014797.3:c.16G>A
  • NM_001161352.2:c.16G>AMANE SELECT
  • NM_001161353.2:c.16G>A
  • NM_001271518.2:c.16G>A
  • NM_001271519.2:c.16G>A
  • NM_001271520.2:c.16G>A
  • NM_001271521.2:c.16G>A
  • NM_001271522.2:c.16G>A
  • NM_001322829.2:c.16G>A
  • NM_001322830.2:c.16G>A
  • NM_001322832.2:c.16G>A
  • NM_001322835.2:c.16G>A
  • NM_001322836.2:c.16G>A
  • NM_001322837.2:c.16G>A
  • NM_001322839.2:c.16G>A
  • NM_002247.4:c.16G>A
  • NP_001014797.1:p.Gly6Ser
  • NP_001154824.1:p.Gly6Ser
  • NP_001154825.1:p.Gly6Ser
  • NP_001258447.1:p.Gly6Ser
  • NP_001258448.1:p.Gly6Ser
  • NP_001258449.1:p.Gly6Ser
  • NP_001258450.1:p.Gly6Ser
  • NP_001258451.1:p.Gly6Ser
  • NP_001309758.1:p.Gly6Ser
  • NP_001309759.1:p.Gly6Ser
  • NP_001309761.1:p.Gly6Ser
  • NP_001309764.1:p.Gly6Ser
  • NP_001309765.1:p.Gly6Ser
  • NP_001309766.1:p.Gly6Ser
  • NP_001309768.1:p.Gly6Ser
  • NP_002238.2:p.Gly6Ser
  • NC_000010.10:g.79397385C>T
  • NM_001014797.2:c.16G>A
  • NM_002247.3:c.16G>A
Protein change:
G6S
Links:
dbSNP: rs914048941
NCBI 1000 Genomes Browser:
rs914048941
Molecular consequence:
  • NM_001014797.3:c.16G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001161352.2:c.16G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001161353.2:c.16G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001271518.2:c.16G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001271519.2:c.16G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001271520.2:c.16G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001271521.2:c.16G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001271522.2:c.16G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322829.2:c.16G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322830.2:c.16G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322832.2:c.16G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322835.2:c.16G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322836.2:c.16G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322837.2:c.16G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001322839.2:c.16G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_002247.4:c.16G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Generalized epilepsy-paroxysmal dyskinesia syndrome (PNKD3)
Synonyms:
Generalized epilepsy and paroxysmal dyskinesia; Paroxysmal nonkinesigenic dyskinesia, 3, with or without generalized epilepsy
Identifiers:
MONDO: MONDO:0012276; MedGen: C5574945; Orphanet: 79137; OMIM: 609446

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000761474Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Nov 16, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000761474.7

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Not Available"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 532940). This variant has not been reported in the literature in individuals affected with KCNMA1-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This sequence change replaces glycine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 6 of the KCNMA1 protein (p.Gly6Ser).

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

Last Updated: Aug 4, 2024