NM_001161352.2(KCNMA1):c.144TTC[3] (p.Ser60del) AND Paroxysmal nonkinesigenic dyskinesia, 3, with or without generalized epilepsy

Clinical significance:Conflicting interpretations of pathogenicity, Benign(1);Uncertain significance(1) (Last evaluated: Dec 2, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, conflicting interpretations

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000340068.5

Allele description [Variation Report for NM_001161352.2(KCNMA1):c.144TTC[3] (p.Ser60del)]

NM_001161352.2(KCNMA1):c.144TTC[3] (p.Ser60del)

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.144TTC[3] (p.Ser60del)
HGVS:
  • NC_000010.11:g.77637490AGA[3]
  • NG_012270.1:g.5321TTC[3]
  • NM_001014797.3:c.144TTC[3]
  • NM_001161352.2:c.144TTC[3]MANE SELECT
  • NM_001161353.2:c.144TTC[3]
  • NM_001271518.2:c.144TTC[3]
  • NM_001271519.2:c.144TTC[3]
  • NM_001271520.2:c.144TTC[3]
  • NM_001271521.2:c.144TTC[3]
  • NM_001271522.2:c.144TTC[3]
  • NM_001322829.2:c.144TTC[3]
  • NM_001322830.2:c.144TTC[3]
  • NM_001322832.2:c.144TTC[3]
  • NM_001322835.2:c.144TTC[3]
  • NM_001322836.2:c.144TTC[3]
  • NM_001322837.2:c.144TTC[3]
  • NM_001322839.2:c.144TTC[3]
  • NM_002247.4:c.144TTC[3]
  • NP_001014797.1:p.Ser60del
  • NP_001154824.1:p.Ser60del
  • NP_001154825.1:p.Ser60del
  • NP_001258447.1:p.Ser60del
  • NP_001258448.1:p.Ser60del
  • NP_001258449.1:p.Ser60del
  • NP_001258450.1:p.Ser60del
  • NP_001258451.1:p.Ser60del
  • NP_001309758.1:p.Ser60del
  • NP_001309759.1:p.Ser60del
  • NP_001309761.1:p.Ser60del
  • NP_001309764.1:p.Ser60del
  • NP_001309765.1:p.Ser60del
  • NP_001309766.1:p.Ser60del
  • NP_001309768.1:p.Ser60del
  • NP_002238.2:p.Ser60del
  • NC_000010.10:g.79397246_79397248del
  • NC_000010.10:g.79397248AGA[3]
  • NM_002247.3:c.153_155del
  • NM_002247.3:c.153_155delTTC
Protein change:
S60del
Links:
dbSNP: rs751901610
NCBI 1000 Genomes Browser:
rs751901610
Molecular consequence:
  • NM_001014797.3:c.144TTC[3] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001161352.2:c.144TTC[3] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001161353.2:c.144TTC[3] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001271518.2:c.144TTC[3] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001271519.2:c.144TTC[3] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001271520.2:c.144TTC[3] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001271521.2:c.144TTC[3] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001271522.2:c.144TTC[3] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001322829.2:c.144TTC[3] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001322830.2:c.144TTC[3] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001322832.2:c.144TTC[3] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001322835.2:c.144TTC[3] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001322836.2:c.144TTC[3] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001322837.2:c.144TTC[3] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001322839.2:c.144TTC[3] - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_002247.4:c.144TTC[3] - inframe_deletion - [Sequence Ontology: SO:0001822]

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
SCV000365136Illumina Clinical Services Laboratory,Illuminacriteria provided, single submitter
Uncertain significance
(Jun 14, 2016)
germlineclinical testing

ICSL_Variant_Classification_20161018.pdf,

Citation Link,

SCV000761482Invitaecriteria provided, single submitter
Benign
(Dec 2, 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 Illumina Clinical Services Laboratory,Illumina, SCV000365136.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
2not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided
2germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Invitae, SCV000761482.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2021

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