rs121908235
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 1P and 5B. PP2BS1_SupportingBS2
The NM_001127222.2(CACNA1A):c.6400C>T(p.Arg2134Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000114 in 1,383,484 control chromosomes in the GnomAD database, including 1 homozygotes. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R2134H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001127222.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CACNA1A | NM_001127222.2 | c.6400C>T | p.Arg2134Cys | missense_variant | 45/47 | ENST00000360228.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CACNA1A | ENST00000360228.11 | c.6400C>T | p.Arg2134Cys | missense_variant | 45/47 | 1 | NM_001127222.2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152174Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000451 AC: 3AN: 66538Hom.: 0 AF XY: 0.0000575 AC XY: 2AN XY: 34754
GnomAD4 exome AF: 0.000119 AC: 147AN: 1231192Hom.: 1 Cov.: 32 AF XY: 0.000120 AC XY: 71AN XY: 593754
GnomAD4 genome ? AF: 0.0000722 AC: 11AN: 152292Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74460
ClinVar
Submissions by phenotype
not provided Uncertain:5
Uncertain significance, criteria provided, single submitter | clinical testing | Athena Diagnostics | Nov 07, 2018 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Aug 15, 2023 | Reported in an individual with episodic ataxia (Mantuano et al., 2004) and an individual with small vessel disease-related stroke (Tan et al., 2019); also reported in an individual with cognitive impairment, behavior disorder, hypophonia and dysarthria (Mariani et al., 2016); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 15173248, 34426522, 31719132, 27400454, 35401678, 28252636) - |
Uncertain significance, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Feb 14, 2020 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2023 | CACNA1A: PP2, PP3 - |
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Dec 21, 2021 | - - |
Episodic ataxia type 2 Uncertain:1Other:1
not provided, no classification provided | literature only | UniProtKB/Swiss-Prot | - | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | New York Genome Center | Apr 18, 2020 | The heterozygous p.Arg2135Cys (also known as p.Arg2136Cys) missense variant identified in CACNA1A has been reported in a patient with episodic ataxia type 2 [PMID: 15173248], and in another individual with developmental delay and spastic diplegia who inherited the variant from asymptomatic father [PMID: 28252636]. The variant has 0.00005107 allele frequency in the gnomAD database (5 out of 97,896 heterozygous alleles) indicating it is a rare allele in the general population. The affected reside is moderately conserved and in silico tools provide conflicting interpretations about pathogenicity of this variant. Functional studies to evaluate the potential pathogenicy of this variant have not been performed to the best of our knowledge. Based on the available evidence, the p.Arg2135Cys variant in the CACNA1A gene is classified as a variant of uncertain significance. - |
Tip-toe gait Pathogenic:1
Likely pathogenic, no assertion criteria provided | clinical testing | Practice for Gait Abnormalities, David Pomarino, Competency Network Toe Walking c/o Practice Pomarino | Jan 11, 2022 | - - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Feb 07, 2023 | Variant summary: CACNA1A c.6403C>T (p.Arg2135Cys) results in a non-conservative amino acid change located in the C-terminal tail, upstream of the polyglutamine repeat (Mantuano_2004). The CACNA1A gene has a bicistronic mRNA, with the first cistron encoding the voltage-gated calcium channel subunit alpha1A and the second cistron expressing the C-terminal fragment of the alpha1A subunit (alpha1ACT), which is a transcription factor (that also contains the polyglutamine tract), and coordinates the expression of genes involved in neural and Purkinje cell development (PMID: 23827678); our variant of interest affects both of these encoded proteins. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 7.3e-05 (i.e. in 11 carriers) in 150946 control chromosomes (gnomAD v3.1, genomes dataset). The variant, c.6403C>T, has also been reported in the literature in heterozygous individuals affected with Episodic ataxia type 2 (Mantuano_2004), Huntington disease-like phenotype (Mariani_2016), small vessel disease-related lacunar stroke (Tan_2019), and spinocerebellar ataxia (Ghorbani_2022). In addition, the variant was also reported in an exome study in a child with developmental delay and spastic diplegia, however the variant was inherited from an asymptomatic father (Baldridge_2017). These reports do not provide unequivocal conclusions about association of the variant with Episodic ataxia. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Nine other clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014, partly without evidence for independent evaluation, and all of them classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance. - |
Spinocerebellar ataxia type 6 Uncertain:1
Uncertain significance, no assertion criteria provided | research | O&I group, Department of Genetics, University Medical Center of Groningen | Jul 22, 2021 | - - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 31, 2018 | The p.R2135C variant (also known as c.6403C>T), located in coding exon 45 of the CACNA1A gene, results from a C to T substitution at nucleotide position 6403. The arginine at codon 2135 is replaced by cysteine, an amino acid with highly dissimilar properties. This alteration has been detected in two individuals in the literature; one with a clinical diagnosis of episodic ataxia type 2 (EA2) and another with Huntingon Disease symptoms who eventually developed cerebellar signs and dysarthria. Of note, this alteration has been called p.R2136C (c.6681C>T) and p.R2140C (c.6418C>T) in the literature (Mantuano E et al. J. Med. Genet., 2004 Jun;41:e82; Mariani LL et al. JAMA Neurol, 2016 Sep;73:1105-14). This amino acid position is well conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Cerebellar ataxia Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Kariminejad - Najmabadi Pathology & Genetics Center | Nov 22, 2018 | - - |
Episodic ataxia type 2;C4310716:Developmental and epileptic encephalopathy, 42 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 22, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at