rs786205748
Variant summary
Our verdict is Pathogenic. Variant got 17 ACMG points: 17P and 0B. PS1_ModeratePM2PM5PP2PP3_ModeratePP5_Very_Strong
The NM_000719.7(CACNA1C):c.1552C>T(p.Arg518Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000693 in 1,443,586 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 11/19 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely pathogenicin UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R518S) has been classified as Likely pathogenic.
Frequency
Consequence
NM_000719.7 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 17 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CACNA1C | NM_000719.7 | c.1552C>T | p.Arg518Cys | missense_variant | 12/47 | ENST00000399655.6 | |
CACNA1C | NM_001167623.2 | c.1552C>T | p.Arg518Cys | missense_variant | 12/47 | ENST00000399603.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CACNA1C | ENST00000399603.6 | c.1552C>T | p.Arg518Cys | missense_variant | 12/47 | 5 | NM_001167623.2 | ||
CACNA1C | ENST00000399655.6 | c.1552C>T | p.Arg518Cys | missense_variant | 12/47 | 1 | NM_000719.7 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 6.93e-7 AC: 1AN: 1443586Hom.: 0 Cov.: 31 AF XY: 0.00000140 AC XY: 1AN XY: 716098
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Long qt syndrome 8 Pathogenic:2
Pathogenic, criteria provided, single submitter | clinical testing | Victorian Clinical Genetics Services, Murdoch Childrens Research Institute | May 06, 2021 | Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0101 - Gain of function is a known mechanism of disease in this gene and is associated with LQTS (MIM#618447) and Timothy syndrome (MIM#601005). Missense variants result in loss of channel inactivation and increased current (OMIM, PMID: 25260352). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0200 - Variant is predicted to result in a missense amino acid change from arginine to cysteine. (I) 0251 - This variant is heterozygous. (I) 0301 - Variant is absent from gnomAD (both v2 and v3). (SP) 0309 - An alternative amino acid change at the same position has been observed in gnomAD (1 heterozygote, 0 homozygotes). (I) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a major amino acid change. (SP) 0600 - Variant is located in the annotated I-II cytoplasmic linker region (PMID: 30513141). (I) 0702 - Other missense variants comparable to the one identified in this case have moderate previous evidence for pathogenicity. These alternative changes (p.Arg518Ser, p.Arg518His) have been reported as likely pathogenic and pathogenic, and have been observed in multiple patients with hypertrophic cardiomyopathy (HCM) and Long QT syndrome (LQTS) (ClinVar, LOVD, PMID: 30513141, 30025578, 32161207). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been reported as pathogenic and likely pathogenic, and has been observed in multiple patients with HCM, LQTS, congenital heart defects and sudden cardiac death (VCGS, LOVD, ClinVar, PMID: 30513141, 29071820, 30984024, 32161207). (SP) 1002 - This variant has moderate functional evidence supporting abnormal protein function. Transfected HEK293 cells have demonstrated both loss of function and gain of function effects on protein function, including slowed channel inactivation (PMID: 30513141). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign - |
Pathogenic, criteria provided, single submitter | clinical testing | 3billion | May 22, 2022 | The variant is not observed in the gnomAD v2.1.1 dataset. Missense changes are a common disease-causing mechanism. Functional studies provide strong evidence of the variant having a damaging effect on the gene or gene product (PMID:26253506). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.88; 3Cnet: 0.86). Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000190642). A different missense change at the same codon (p.Arg518His) has been reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000372313). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline. - |
not provided Pathogenic:2
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Mar 14, 2019 | Described in another individual with LQTS and a positive family history, though segregation data was not provided (Seo et al., 2018); Reported in ClinVar as pathogenic (ClinVar Variant ID# 190642; Landrum et al., 2016); Not observed in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Whole cell patch clamp studies revealed a complex phenotype, including loss of current density and inactivation in combination with increased window and late current (Boczek et al., 2015); This variant is associated with the following publications: (PMID: 27390944, 26253506, 30513141, 29071820, 30172029, 30345660, 31430211, 32161207) - |
Likely pathogenic, no assertion criteria provided | provider interpretation | Stanford Center for Inherited Cardiovascular Disease, Stanford University | Apr 14, 2016 | - - |
Timothy syndrome Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Sep 29, 2022 | - - |
Long QT syndrome Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Jan 16, 2024 | This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 518 of the CACNA1C protein (p.Arg518Cys). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with long QT syndrome (LQTS), hypertrophic cardiomyopathy (HCM) and septal defects (CHD) (PMID: 26253506; Invitae). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 190642). 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 CACNA1C protein function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects CACNA1C function (PMID: 26253506). For these reasons, this variant has been classified as Pathogenic. - |
Cardiovascular phenotype Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 22, 2021 | The p.R518C pathogenic mutation (also known as c.1552C>T), located in coding exon 12 of the CACNA1C gene, results from a C to T substitution at nucleotide position 1552. The arginine at codon 518 is replaced by cysteine, an amino acid with highly dissimilar properties. This alteration has been reported in multiple unrelated probands with mixed cardiac phenotypes, including long QT syndrome, hypertrophic cardiomyopathy, cardiac conduction defects, and congenital heart disease, and has been reported to segregate with disease in several families (Boczek NJ et al. Circ Arrhythm Electrophysiol, 2015 Oct;8:1122-32; Seo SH et al. Ann Lab Med, 2018 Jan;38:54-58; Korkosh VS et al. Front Physiol, 2019 Mar;10:335; Fukuyama M et al. Circ J, 2020 03;84:559-568; GeneDx pers comm; Invitae pers comm; Ambry internal data). Functional studies performed in vitro indicate that R518C leads to a decrease in peak channel current density but an increase in the late calcium current (Boczek NJ et al. Circ Arrhythm Electrophysiol, 2015 Oct;8:1122-32; Estes SI et al. Circ Genom Precis Med, 2019 08;12:e002534). Another pathogenic alteration, p.R518H, has been described in the same codon (Boczek NJ et al. Circ Arrhythm Electrophysiol, 2015 Oct;8:1122-32). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at