NM_001161352.2(KCNMA1):c.1320C>T (p.Ile440=) AND Generalized epilepsy-paroxysmal dyskinesia syndrome

Germline classification:: Benign/Likely benign (4 submissions)
Last evaluated:: Jan 30, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000388522.17

Allele description [Variation Report for NM_001161352.2(KCNMA1):c.1320C>T (p.Ile440=)]

NM_001161352.2(KCNMA1):c.1320C>T (p.Ile440=)

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.1320C>T (p.Ile440=)

HGVS:

NC_000010.11:g.77090414G>A
NG_012270.1:g.552406C>T
NM_001014797.3:c.1320C>T
NM_001161352.2:c.1320C>TMANE SELECT
NM_001161353.2:c.1320C>T
NM_001271518.2:c.1158C>T
NM_001271519.2:c.1320C>T
NM_001322829.2:c.1320C>T
NM_001322830.2:c.1320C>T
NM_001322832.2:c.1320C>T
NM_001322835.2:c.1320C>T
NM_001322836.2:c.1320C>T
NM_001322837.2:c.1320C>T
NM_001322838.2:c.780C>T
NM_002247.4:c.1320C>T
NP_001014797.1:p.Ile440=
NP_001154824.1:p.Ile440=
NP_001154825.1:p.Ile440=
NP_001258447.1:p.Ile386=
NP_001258448.1:p.Ile440=
NP_001309758.1:p.Ile440=
NP_001309759.1:p.Ile440=
NP_001309761.1:p.Ile440=
NP_001309764.1:p.Ile440=
NP_001309765.1:p.Ile440=
NP_001309766.1:p.Ile440=
NP_001309767.1:p.Ile260=
NP_002238.2:p.Ile440=
NC_000010.10:g.78850172G>A
NM_001014797.2:c.1320C>T
NM_001322830.1:c.1320C>T
NM_002247.3:c.1320C>T
p.Ile440Ile

Links:

dbSNP: rs45617636

NCBI 1000 Genomes Browser:

rs45617636

Molecular consequence:

NM_001014797.3:c.1320C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001161352.2:c.1320C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001161353.2:c.1320C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001271518.2:c.1158C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001271519.2:c.1320C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322829.2:c.1320C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322830.2:c.1320C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322832.2:c.1320C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322835.2:c.1320C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322836.2:c.1320C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322837.2:c.1320C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_001322838.2:c.780C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_002247.4:c.1320C>T - synonymous variant - [Sequence Ontology: SO:0001819]

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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Chain A, Aryl hydrocarbon receptor nuclear translocator-like protein 1
Chain A, Aryl hydrocarbon receptor nuclear translocator-like protein 1
gi|433286790|pdb|4H10|A

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000365128	Illumina Laboratory Services, Illumina	criteria provided, single submitter (ICSL Variant Classification Criteria 13 December 2019)	Likely benign (Jan 12, 2018)	germline	clinical testing	Citation Link,
SCV000638698	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Benign (Jan 30, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000743906	Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus	criteria provided, single submitter (ACGS Guidelines, 2013)	Likely benign (Oct 5, 2016)	germline	clinical testing	Citation Link,
SCV000745339	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus	criteria provided, single submitter (ACGS Guidelines, 2013)	Likely benign (Aug 2, 2017)	germline	clinical testing	Citation Link

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Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical 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 Illumina Laboratory Services, Illumina, SCV000365128.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000638698.7

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus, SCV000743906.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV000745339.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 20, 2024

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