NM_001161352.2(KCNMA1):c.36CGG[8] (p.Gly20dup) AND Paroxysmal nonkinesigenic dyskinesia, 3, with or without generalized epilepsy

Clinical significance:Uncertain significance (Last evaluated: Oct 19, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000548229.4

Allele description [Variation Report for NM_001161352.2(KCNMA1):c.36CGG[8] (p.Gly20dup)]

NM_001161352.2(KCNMA1):c.36CGG[8] (p.Gly20dup)

Gene:
KCNMA1:potassium calcium-activated channel subfamily M alpha 1 [Gene - OMIM - HGNC]
Variant type:
Microsatellite
Cytogenetic location:
10q22.3
Genomic location:
Preferred name:
NM_001161352.2(KCNMA1):c.36CGG[8] (p.Gly20dup)
HGVS:
  • NC_000010.11:g.77637588CGC[8]
  • NG_012270.1:g.5213CGG[8]
  • NM_001014797.3:c.36CGG[8]
  • NM_001161352.2:c.36CGG[8]MANE SELECT
  • NM_001161353.2:c.36CGG[8]
  • NM_001271518.2:c.36CGG[8]
  • NM_001271519.2:c.36CGG[8]
  • NM_001271520.2:c.36CGG[8]
  • NM_001271521.2:c.36CGG[8]
  • NM_001271522.2:c.36CGG[8]
  • NM_001322829.2:c.36CGG[8]
  • NM_001322830.2:c.36CGG[8]
  • NM_001322832.2:c.36CGG[8]
  • NM_001322835.2:c.36CGG[8]
  • NM_001322836.2:c.36CGG[8]
  • NM_001322837.2:c.36CGG[8]
  • NM_001322839.2:c.36CGG[8]
  • NM_002247.4:c.36CGG[8]
  • NP_001014797.1:p.Gly20dup
  • NP_001154824.1:p.Gly20dup
  • NP_001154825.1:p.Gly20dup
  • NP_001258447.1:p.Gly20dup
  • NP_001258448.1:p.Gly20dup
  • NP_001258449.1:p.Gly20dup
  • NP_001258450.1:p.Gly20dup
  • NP_001258451.1:p.Gly20dup
  • NP_001309758.1:p.Gly20dup
  • NP_001309759.1:p.Gly20dup
  • NP_001309761.1:p.Gly20dup
  • NP_001309764.1:p.Gly20dup
  • NP_001309765.1:p.Gly20dup
  • NP_001309766.1:p.Gly20dup
  • NP_001309768.1:p.Gly20dup
  • NP_002238.2:p.Gly20dup
  • NC_000010.10:g.79397346CGC[8]
  • NM_002247.3:c.54_56dup
  • NM_002247.3:c.54_56dup
  • NM_002247.3:c.54_56dupCGG
  • p.Gly20dup
Links:
dbSNP: rs760628050
NCBI 1000 Genomes Browser:
rs760628050
Molecular consequence:
  • NM_001014797.3:c.36CGG[8] - inframe_insertion - [Sequence Ontology: SO:0001821]
  • NM_001161352.2:c.36CGG[8] - inframe_insertion - [Sequence Ontology: SO:0001821]
  • NM_001161353.2:c.36CGG[8] - inframe_insertion - [Sequence Ontology: SO:0001821]
  • NM_001271518.2:c.36CGG[8] - inframe_insertion - [Sequence Ontology: SO:0001821]
  • NM_001271519.2:c.36CGG[8] - inframe_insertion - [Sequence Ontology: SO:0001821]
  • NM_001271520.2:c.36CGG[8] - inframe_insertion - [Sequence Ontology: SO:0001821]
  • NM_001271521.2:c.36CGG[8] - inframe_insertion - [Sequence Ontology: SO:0001821]
  • NM_001271522.2:c.36CGG[8] - inframe_insertion - [Sequence Ontology: SO:0001821]
  • NM_001322829.2:c.36CGG[8] - inframe_insertion - [Sequence Ontology: SO:0001821]
  • NM_001322830.2:c.36CGG[8] - inframe_insertion - [Sequence Ontology: SO:0001821]
  • NM_001322832.2:c.36CGG[8] - inframe_insertion - [Sequence Ontology: SO:0001821]
  • NM_001322835.2:c.36CGG[8] - inframe_insertion - [Sequence Ontology: SO:0001821]
  • NM_001322836.2:c.36CGG[8] - inframe_insertion - [Sequence Ontology: SO:0001821]
  • NM_001322837.2:c.36CGG[8] - inframe_insertion - [Sequence Ontology: SO:0001821]
  • NM_001322839.2:c.36CGG[8] - inframe_insertion - [Sequence Ontology: SO:0001821]
  • NM_002247.4:c.36CGG[8] - inframe_insertion - [Sequence Ontology: SO:0001821]

Condition(s)

Name:
Paroxysmal nonkinesigenic dyskinesia, 3, with or without generalized epilepsy (PNKD3)
Synonyms:
Generalized epilepsy and paroxysmal dyskinesia
Identifiers:
MONDO: MONDO:0012276; MedGen: C1836173; Orphanet: 79137; OMIM: 609446

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000638721Invitaecriteria provided, single submitter
Uncertain significance
(Oct 19, 2020)
germlineclinical testing

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

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):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Invitae, SCV000638721.4

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

Description

This variant, c.54_56dup, results in the insertion of 1 amino acid(s) to the KCNMA1 protein (p.Gly20dup), but otherwise preserves the integrity of the reading frame. While this variant is present in population databases (rs760628050), the frequency information is unreliable, as metrics indicate poor data quality at this position in the ExAC database. This variant has not been reported in the literature in individuals with KCNMA1-related conditions. ClinVar contains an entry for this variant (Variation ID: 193225). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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.

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

Last Updated: Aug 21, 2021

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