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NM_001127222.2(CACNA1A):c.601C>T (p.Arg201Trp) AND multiple conditions

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Aug 31, 2022
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:
RCV001896526.6

Allele description [Variation Report for NM_001127222.2(CACNA1A):c.601C>T (p.Arg201Trp)]

NM_001127222.2(CACNA1A):c.601C>T (p.Arg201Trp)

Gene:
CACNA1A:calcium voltage-gated channel subunit alpha1 A [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
19p13.13
Genomic location:
Preferred name:
NM_001127222.2(CACNA1A):c.601C>T (p.Arg201Trp)
HGVS:
  • NC_000019.10:g.13371718G>A
  • NG_011569.1:g.139743C>T
  • NM_000068.4:c.601C>T
  • NM_001127221.2:c.601C>T
  • NM_001127222.2:c.601C>TMANE SELECT
  • NM_001174080.2:c.601C>T
  • NM_023035.3:c.601C>T
  • NP_000059.3:p.Arg201Trp
  • NP_001120693.1:p.Arg201Trp
  • NP_001120694.1:p.Arg201Trp
  • NP_001167551.1:p.Arg201Trp
  • NP_075461.2:p.Arg201Trp
  • LRG_7:g.139743C>T
  • NC_000019.9:g.13482532G>A
Protein change:
R201W
Links:
dbSNP: rs2144559282
NCBI 1000 Genomes Browser:
rs2144559282
Molecular consequence:
  • NM_000068.4:c.601C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001127221.2:c.601C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001127222.2:c.601C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001174080.2:c.601C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_023035.3:c.601C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Episodic ataxia type 2 (EA2)
Synonyms:
Episodic ataxia with nystagmus; Nystagmus-associated episodic ataxia; Cerebellopathy, hereditary paroxysmal; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0007163; MedGen: C1720416; Orphanet: 97; OMIM: 108500
Name:
Developmental and epileptic encephalopathy, 42 (DEE42)
Synonyms:
Epileptic encephalopathy, early infantile, 42
Identifiers:
MONDO: MONDO:0014917; MedGen: C4310716; OMIM: 617106

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002167166Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Aug 31, 2022) 		germlineclinical testing

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

Help

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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002167166.3

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

Description

Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt CACNA1A protein function. ClinVar contains an entry for this variant (Variation ID: 1393036). This variant has not been reported in the literature in individuals affected with CACNA1A-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 201 of the CACNA1A protein (p.Arg201Trp). 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: Sep 29, 2024