rs952757731
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP2BP4
The NM_001127222.2(CACNA1A):c.29C>T(p.Ala10Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000334 in 1,498,646 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_001127222.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CACNA1A | NM_001127222.2 | c.29C>T | p.Ala10Val | missense_variant | 1/47 | ENST00000360228.11 | NP_001120694.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CACNA1A | ENST00000360228.11 | c.29C>T | p.Ala10Val | missense_variant | 1/47 | 1 | NM_001127222.2 | ENSP00000353362.5 | ||
CACNA1A | ENST00000638029.1 | c.29C>T | p.Ala10Val | missense_variant | 1/48 | 5 | ENSP00000489829.1 | |||
CACNA1A | ENST00000573710.7 | c.29C>T | p.Ala10Val | missense_variant | 1/47 | 5 | ENSP00000460092.3 | |||
CACNA1A | ENST00000635727.1 | c.29C>T | p.Ala10Val | missense_variant | 1/47 | 5 | ENSP00000490001.1 | |||
CACNA1A | ENST00000637769.1 | c.29C>T | p.Ala10Val | missense_variant | 1/47 | 1 | ENSP00000489778.1 | |||
CACNA1A | ENST00000636012.1 | c.29C>T | p.Ala10Val | missense_variant | 1/46 | 5 | ENSP00000490223.1 | |||
CACNA1A | ENST00000637736.1 | c.29C>T | p.Ala10Val | missense_variant | 1/46 | 5 | ENSP00000489861.1 | |||
CACNA1A | ENST00000636389.1 | c.29C>T | p.Ala10Val | missense_variant | 1/47 | 5 | ENSP00000489992.1 | |||
CACNA1A | ENST00000637432.1 | c.29C>T | p.Ala10Val | missense_variant | 1/48 | 5 | ENSP00000490617.1 | |||
CACNA1A | ENST00000636549.1 | c.29C>T | p.Ala10Val | missense_variant | 1/48 | 5 | ENSP00000490578.1 | |||
CACNA1A | ENST00000637927.1 | c.29C>T | p.Ala10Val | missense_variant | 1/47 | 5 | ENSP00000489715.1 | |||
CACNA1A | ENST00000635895.1 | c.29C>T | p.Ala10Val | missense_variant | 1/47 | 5 | ENSP00000490323.1 | |||
CACNA1A | ENST00000638009.2 | c.29C>T | p.Ala10Val | missense_variant | 1/47 | 1 | ENSP00000489913.1 | |||
CACNA1A | ENST00000637276.1 | c.29C>T | p.Ala10Val | missense_variant | 1/46 | 5 | ENSP00000489777.1 |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152150Hom.: 0 Cov.: 30
GnomAD4 exome AF: 0.00000149 AC: 2AN: 1346496Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 661814
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152150Hom.: 0 Cov.: 30 AF XY: 0.0000135 AC XY: 1AN XY: 74312
ClinVar
Submissions by phenotype
Episodic ataxia type 2;C4310716:Developmental and epileptic encephalopathy, 42 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 02, 2023 | This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 10 of the CACNA1A protein (p.Ala10Val). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with CACNA1A-related conditions. ClinVar contains an entry for this variant (Variation ID: 422558). 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 not expected to disrupt CACNA1A protein function with a negative predictive value of 95%. 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. - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 01, 2023 | The c.29C>T (p.A10V) alteration is located in exon 1 (coding exon 1) of the CACNA1A gene. This alteration results from a C to T substitution at nucleotide position 29, causing the alanine (A) at amino acid position 10 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Jun 12, 2017 | The A10V variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The A10V variant is not observed in large population cohorts; however, limited data are available (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The A10V variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties, and this substitution occurs at a position that is not conserved. However, in silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant. - |
Developmental and epileptic encephalopathy, 42 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | New York Genome Center | Mar 05, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at