rs150590855
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 6P and 1B. PM1PM2PM5BP6
The NM_000069.3(CACNA1S):c.1493G>T(p.Arg498Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000927 in 1,614,166 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. R498H) has been classified as Pathogenic.
Frequency
Consequence
NM_000069.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CACNA1S | NM_000069.3 | c.1493G>T | p.Arg498Leu | missense_variant | 11/44 | ENST00000362061.4 | NP_000060.2 | |
CACNA1S | XM_005245478.4 | c.1493G>T | p.Arg498Leu | missense_variant | 11/43 | XP_005245535.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CACNA1S | ENST00000362061.4 | c.1493G>T | p.Arg498Leu | missense_variant | 11/44 | 1 | NM_000069.3 | ENSP00000355192 | P2 |
Frequencies
GnomAD3 genomes AF: 0.000565 AC: 86AN: 152214Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000561 AC: 141AN: 251488Hom.: 0 AF XY: 0.000537 AC XY: 73AN XY: 135920
GnomAD4 exome AF: 0.000965 AC: 1410AN: 1461834Hom.: 1 Cov.: 35 AF XY: 0.000916 AC XY: 666AN XY: 727216
GnomAD4 genome AF: 0.000565 AC: 86AN: 152332Hom.: 0 Cov.: 31 AF XY: 0.000550 AC XY: 41AN XY: 74490
ClinVar
Submissions by phenotype
not provided Uncertain:3
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Jun 30, 2023 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Nov 01, 2023 | Reported previously in an individual with malignant hyperthermia susceptibility (PMID: 25735680); Reported previously in an individual with Takotsubo cardiomyopathy that underwent whole exome sequencing; however, CACNA1S was only reported as a candidate gene and other potentially pathogenic variants were also reported in this individual (PMID: 25132214); Reported previously as a variant of uncertain significance in a patient with recurrent exertional rhabdomyolysis and possible malignant hyperthermia susceptibility; this patient also had a pathogenic variant in a different gene related to a separate diagnosis (PMID: 30094188); 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: 32054689, 25132214, 25735680, 30094188) - |
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Mar 01, 2024 | CACNA1S: PP3 - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Athena Diagnostics | Mar 31, 2017 | - - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 03, 2022 | The c.1493G>T (p.R498L) alteration is located in exon 11 (coding exon 11) of the CACNA1S gene. This alteration results from a G to T substitution at nucleotide position 1493, causing the arginine (R) at amino acid position 498 to be replaced by a leucine (L). Based on data from gnomAD, the T allele has an overall frequency of 0.06% (168/282898) total alleles studied. The highest observed frequency was 0.1% (127/129198) of European (non-Finnish) alleles. This alteration was reported to be heterozygous in an individual with malignant hyperthermia susceptibility with positive in vitro contracture tests (Gillies, 2015). This amino acid position is highly conserved in available vertebrate species. The p.R498L alteration is predicted to be deleterious by in silico analysis. Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Malignant hyperthermia, susceptibility to, 5 Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | Knight Diagnostic Laboratories, Oregon Health and Sciences University | Sep 26, 2015 | - - |
Hypokalemic periodic paralysis, type 1 Benign:1
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | 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 benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Malignant hyperthermia, susceptibility to, 5;C3714580:Hypokalemic periodic paralysis, type 1 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 18, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at