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NM_001161352.2(KCNMA1):c.1334+3A>G AND Generalized epilepsy-paroxysmal dyskinesia syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Apr 24, 2021
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:
RCV001986986.4

Allele description [Variation Report for NM_001161352.2(KCNMA1):c.1334+3A>G]

NM_001161352.2(KCNMA1):c.1334+3A>G

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.1334+3A>G
HGVS:
  • NC_000010.11:g.77090397T>C
  • NG_012270.1:g.552423A>G
  • NM_001014797.3:c.1334+3A>G
  • NM_001161352.2:c.1334+3A>GMANE SELECT
  • NM_001161353.2:c.1334+3A>G
  • NM_001271518.2:c.1172+3A>G
  • NM_001271519.2:c.1334+3A>G
  • NM_001322829.2:c.1334+3A>G
  • NM_001322830.2:c.1334+3A>G
  • NM_001322832.2:c.1334+3A>G
  • NM_001322835.2:c.1334+3A>G
  • NM_001322836.2:c.1334+3A>G
  • NM_001322837.2:c.1334+3A>G
  • NM_001322838.2:c.794+3A>G
  • NM_002247.4:c.1334+3A>G
  • NC_000010.10:g.78850155T>C
Links:
dbSNP: rs2153792200
NCBI 1000 Genomes Browser:
rs2153792200
Molecular consequence:
  • NM_001014797.3:c.1334+3A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001161352.2:c.1334+3A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001161353.2:c.1334+3A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001271518.2:c.1172+3A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001271519.2:c.1334+3A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322829.2:c.1334+3A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322830.2:c.1334+3A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322832.2:c.1334+3A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322835.2:c.1334+3A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322836.2:c.1334+3A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322837.2:c.1334+3A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001322838.2:c.794+3A>G - intron variant - [Sequence Ontology: SO:0001627]
  • NM_002247.4:c.1334+3A>G - intron variant - [Sequence Ontology: SO:0001627]

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
SCV002277720Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Apr 24, 2021) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Aberrant 5' splice sites in human disease genes: mutation pattern, nucleotide structure and comparison of computational tools that predict their utilization.

Buratti E, Chivers M, Královicová J, Romano M, Baralle M, Krainer AR, Vorechovsky I.

Nucleic Acids Res. 2007;35(13):4250-63. Epub 2007 Jun 18.

PubMed [citation]
PMID:
17576681
PMCID:
PMC1934990

Statistical features of human exons and their flanking regions.

Zhang MQ.

Hum Mol Genet. 1998 May;7(5):919-32.

PubMed [citation]
PMID:
9536098
See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002277720.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

This variant is not present in population databases (ExAC no frequency). This sequence change falls in intron 10 of the KCNMA1 gene. It does not directly change the encoded amino acid sequence of the KCNMA1 protein. It affects a nucleotide within the consensus splice site of the intron. This variant has not been reported in the literature in individuals with KCNMA1-related conditions. 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. Nucleotide substitutions within the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site, but this prediction has not been confirmed by published transcriptional studies.

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

Last Updated: Oct 13, 2024