NM_000217.3(KCNA1):c.44C>T (p.Ala15Val) AND Episodic ataxia type 1

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 9, 2024
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:: RCV002800709.4

Allele description [Variation Report for NM_000217.3(KCNA1):c.44C>T (p.Ala15Val)]

NM_000217.3(KCNA1):c.44C>T (p.Ala15Val)

Genes:

LOC130007218:ATAC-STARR-seq lymphoblastoid silent region 4155 [Gene]
KCNA1:potassium voltage-gated channel subfamily A member 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

12p13.32

Genomic location:

Preferred name:

NM_000217.3(KCNA1):c.44C>T (p.Ala15Val)

HGVS:

NC_000012.12:g.4911422C>T
NG_011815.1:g.6516C>T
NM_000217.3:c.44C>TMANE SELECT
NP_000208.2:p.Ala15Val
LRG_1297t1:c.44C>T
LRG_1297:g.6516C>T
LRG_1297p1:p.Ala15Val
NC_000012.11:g.5020588C>T

Protein change:

A15V

Molecular consequence:

NM_000217.3:c.44C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Episodic ataxia type 1 (EA1)
Synonyms:: ATAXIA, EPISODIC, WITH MYOKYMIA; MYOKYMIA WITH PERIODIC ATAXIA; PAROXYSMAL ATAXIA WITH NEUROMYOTONIA, HEREDITARY; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0008047; MedGen: C1719788; Orphanet: 972; OMIM: 160120

Recent activity

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Mus musculus 3 days neonate thymus cDNA, RIKEN full-length enriched library, clo...
Mus musculus 3 days neonate thymus cDNA, RIKEN full-length enriched library, clone:A630084M22 product:ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 7 (ADP-RIBOSYLATION FACTOR-LIKE PROTEIN LAK) homolog [Homo sapiens], full insert sequence
gi|26348520|dbj|AK080380.1|

Nucleotide
dTDP-glucose 4,6-dehydratase [Escherichia coli]
dTDP-glucose 4,6-dehydratase [Escherichia coli]
gi|2776372162|ref|WP_367745147.1|

Protein
capsule biosynthesis protein [Escherichia coli]
capsule biosynthesis protein [Escherichia coli]
gi|2776388348|ref|WP_367760557.1|

Protein
glutamate-5-semialdehyde dehydrogenase [Escherichia coli]
glutamate-5-semialdehyde dehydrogenase [Escherichia coli]
gi|2776426786|ref|WP_367775636.1|

Protein
esterase [Escherichia coli]
esterase [Escherichia coli]
gi|2776371933|ref|WP_367744924.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003029255	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 9, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003029255

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 9, 2024)

germline

clinical testing

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

Help

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

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV003029255.2

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

Description

This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 15 of the KCNA1 protein (p.Ala15Val). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with KCNA1-related conditions. ClinVar contains an entry for this variant (Variation ID: 1990086). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant¬†is likely to be tolerated. 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.

#	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

Last Updated: Sep 29, 2024

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