rs79891110

chr12-2504944-G-Achr12-2504944-G-T

Variant summary

Our verdict is Pathogenic. Variant got 15 ACMG points: 15P and 0B. PM1 PM2 PP2 PP3_Moderate PP5_Very_Strong

The NM_000719.7(CACNA1C):c.1216G>A(p.Gly406Arg) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000657 in 152,172 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 14/22 in silico tools predict a damaging outcome for this variant. 2/3 splice prediction tools predict no significant impact on normal splicing. 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.

• Frequency:
  • Genomes: 𝑓 0.0000066 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: CACNA1C NM_000719.7 missense, splice_region
• Scores: Splicing: ADA: 0.9697
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:11 O:2
• Conservation: PhyloP100: 10.0

Genes affected

CACNA1C (HGNC:1390): (calcium voltage-gated channel subunit alpha1 C) This gene encodes an alpha-1 subunit of a voltage-dependent calcium channel. Calcium channels mediate the influx of calcium ions into the cell upon membrane polarization. The alpha-1 subunit consists of 24 transmembrane segments and forms the pore through which ions pass into the cell. The calcium channel consists of a complex of alpha-1, alpha-2/delta, beta, and gamma subunits in a 1:1:1:1 ratio. There are multiple isoforms of each of these proteins, either encoded by different genes or the result of alternative splicing of transcripts. The protein encoded by this gene binds to and is inhibited by dihydropyridine. Alternative splicing results in many transcript variants encoding different proteins. Some of the predicted proteins may not produce functional ion channel subunits. [provided by RefSeq, Oct 2012]

ACMG classification

Verdict is Pathogenic. Variant got 15 ACMG points.

• PM1: In a hotspot region, there are 2 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 4 uncertain in NM_000719.7
• PM2: Very rare variant in population databases, with high coverage
• PP2: Missense variant where missense usually causes diseases, CACNA1C
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.936
• PP5: Variant 12-2504944-G-A is Pathogenic according to our data. Variant chr12-2504944-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 17632.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr12-2504944-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CACNA1C	NM_000719.7	c.1216G>A	p.Gly406Arg	missense_variant, splice_region_variant	8/47	ENST00000399655.6
CACNA1C	NM_001167623.2	c.1217+405G>A		intron_variant		ENST00000399603.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CACNA1C	ENST00000399655.6	c.1216G>A	p.Gly406Arg	missense_variant, splice_region_variant	8/47	1	NM_000719.7
CACNA1C	ENST00000399603.6	c.1217+405G>A		intron_variant		5	NM_001167623.2

Frequencies

GnomAD3 genomes AF: 0.00000658 AC: 1 AN: 152054 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000209

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 1312642 Hom.: 0 Cov.: 21 AF XY: 0.00 AC XY: 0 AN XY: 661428

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.00000657 AC: 1 AN: 152172 Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1 AN XY: 74392

Gnomad4 AFR AF: 0.00

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000209

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:11 Other:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:4

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Aug 23, 2018	The G406R variant in the CACNA1C gene has been reported previously in association with Timothy syndrome (Splawski I et al., 2004; Yarotskyy V et al., 2009). Splawski et al. (2004) reported G406R as a de novo variant in 11 unrelated individuals with Timothy syndrome and additionally in two siblings that inherited G406R as a result of germline mosaicism. In this same study, G406R was absent in 360 control alleles and expression of the CACNA1C gene was found in multiple tissue types that correlate to the organ systems affected in Timothy syndrome. Moreover, G406R was not observed in approximately 6,000 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The G406 residue is highly conserved across species and functional studies identified that G406R has a significant effect on calcium ion channel currents leading to action potential prolongation (Splawski I et al., 2004). G406R is a non-conservative amino acid substitution as these residues differ in polarity, charge, size and/or other properties and is more likely to impact secondary structure.In summary, G406R in the CACNA1C gene is interpreted as a disease-causing variant. -
Pathogenic, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Pathogenic, no assertion criteria provided	clinical testing	Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	-	- -
Pathogenic, no assertion criteria provided	provider interpretation	Stanford Center for Inherited Cardiovascular Disease, Stanford University	Apr 25, 2016	- -

Timothy syndrome Pathogenic:2 Other:1

Pathogenic, no assertion criteria provided	literature only	OMIM	Mar 10, 2011	- -
not provided, no classification provided	literature only	GeneReviews	-	Classic Timothy syndrome phenotype -
Pathogenic, criteria provided, single submitter	clinical testing	Center For Human Genetics And Laboratory Diagnostics, Dr. Klein, Dr. Rost And Colleagues	Apr 04, 2018	- -

Timothy syndrome;C2678478:Brugada syndrome 3;C5774213:Neurodevelopmental disorder with hypotonia, language delay, and skeletal defects with or without seizures;CN260585:Long qt syndrome 8 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago

Dec 21, 2022

This variant, located in the alternatively spliced exon 8A of the CACNA1C gene, is a well-established pathogenic variant that is referenced in the GeneReviews article for CACNA1C-Related Disorders as the predominant cause of classic Timothy syndrome (Napolitano 2021 PMID: 20301577). It has been reported in the literature and in ClinVar in numerous individuals with Timothy syndrome, including several instances of this variant as either de novo or mosaic; additionally, multiple individuals are reported to have inherited this variant from unaffected or mildly affected parents as a result of low-level somatic and/or germline mosaicism (Selected publications: Splawski 2004 PMID: 15454078; Etheridge 2011 PIMD: 21910241; Dufendach 2013 PMID: 23690510; Kawaida 2016 PMID: 27593853; Walsh 2018 PIMD: 28371864; ClinVar Variation ID: 17632). It is present in a single heterozygote in the Genome Aggregation Database (Highest reported MAF: 0.02% [1/4784]; https://gnomad.broadinstitute.org/variant/12-2504944-G-A?dataset=gnomad_r3); please note, disease-causing variants may be present in control databases at low frequencies, reflective of the general population, incomplete penetrance, and/or variable expressivity. In vitro functional studies demonstrate a deleterious effect of this variant on calcium channel function (Selected publications: Splawski 2004 PMID: 15454078; Yarotskyy 2009 PMID: 19074970). A mouse model with this variant recapitulated various abnormal neurodevelopmental features seen in individuals with Timothy syndrome (Bader 2011 PIMD: 21878566). Evolutionary conservation and computational prediction tools strongly support that this variant impacts the protein. In summary, this variant is classified as pathogenic. -

CACNA1C-related disorder Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego

Feb 13, 2019

This variant is located in the last amino acid of exon 8. This variant has been previously reported in multiple studies as a de novo heterozygous change in patients with Timothy Syndrome (PMID: 28371864, 23690510, 28211989, 15454078). A functional study showed this variant impairs voltage-dependent channel inactivation causing maintained inward calcium currents (PMID: 15454078). It is absent from the ExAC and gnomAD population databases and thus is presumed to be rare. The c.1216G>A (p.Gly406Arg) variant affects a highly conserved amino acid and is predicted by multiple in silico tools to have a deleterious effect on protein function. Based on the available evidence, the c.1216G>A (p.Gly406Arg) variant is classified as pathogenic. -

Long qt syndrome 8 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Baylor Genetics

Aug 29, 2023

- -

Long QT syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Sep 13, 2022

This variant is not present in population databases (gnomAD no frequency). For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. Experimental studies have shown that this missense change affects CACNA1C function (PMID: 15454078, 15863612, 18250309, 19074970, 26822303). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C15"). ClinVar contains an entry for this variant (Variation ID: 17632). This missense change has been observed in individual(s) with Timothy syndrome (PMID: 15454078, 15863612, 21910241, 23578275, 23580742, 23690510, 26227324). In at least one individual the variant was observed to be de novo. This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 406 of the CACNA1C protein (p.Gly406Arg). -

Cardiovascular phenotype Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

May 03, 2022

The p.G406R pathogenic mutation (also known as c.1216G>A), located in coding exon 8A of the CACNA1C gene, results from a G to A substitution at nucleotide position 1216. The glycine at codon 406 is replaced by arginine, an amino acid with dissimilar properties. This mutation has been detected in numerous individuals with Timothy syndrome (TS), including de novo cases and those due to parental mosaicism; incomplete TS has been described in some cases of somatic mosaicism with this mutation (Splawski I et al. Cell, 2004 Oct;119:19-31; Etheridge SP et al. Am. J. Med. Genet. A, 2011 Oct;155A:2578-83; An HS et al. J. Korean Med. Sci., 2013 May;28:788-91;Dufendach KA et al. Pediatrics, 2013 Jun;131:e1991-5; Walsh MA et al. Europace, 2018 02;20:377-385). Functional studies demonstrated altered gating kinetics and prolonged action potential duration, while mouse models with this mutation showed neurobehavioral and brain changes consistent with TS clinical findings (Splawski I et al. Cell, 2004 Oct;119:19-31; Bader PL et al. Proc. Natl. Acad. Sci. U.S.A., 2011 Sep;108:15432-7; Krey JF et al. Nat. Neurosci., 2013 Feb;16:201-9). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Congenital long QT syndrome Other:1

not provided, no classification provided

literature only

Cardiovascular Biomedical Research Unit, Royal Brompton & Harefield NHS Foundation Trust

-

This variant has been reported in the following publications (PMID:15454078;PMID:15863612;PMID:17224476;PMID:19074970;PMID:21878566). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CardioboostArm	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.54	D
BayesDel_noAF	Pathogenic	0.54
Cadd	Pathogenic	35
Dann	Pathogenic	1.0
DEOGEN2	Uncertain	0.68	D;.;.;.;.;.;.;.;.;.;.;.;.;.;.;T;.;.
Eigen	Pathogenic	1.0
Eigen_PC	Pathogenic	0.95
FATHMM_MKL	Pathogenic	1.0	D
M_CAP	Pathogenic	0.80	D
MetaRNN	Pathogenic	0.94	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM	Pathogenic	1.1	D
MutationTaster	Benign	1.0	A;A;A;A;A;A;A;A;A;A;A;A;A;A;A;A;A;A;A;A;A;A;A
PrimateAI	Pathogenic	0.96	D
PROVEAN	Pathogenic	-6.8	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
REVEL	Pathogenic	0.96
Sift	Uncertain	0.0050	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
Sift4G	Uncertain	0.023	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
Polyphen		1.0, 0.96	.;D;.;D;D;D;D;D;D;D;D;D;D;D;D;.;D;D
Vest4		0.95
MutPred		0.71		Loss of ubiquitination at K410 (P = 0.0816);Loss of ubiquitination at K410 (P = 0.0816);Loss of ubiquitination at K410 (P = 0.0816);Loss of ubiquitination at K410 (P = 0.0816);Loss of ubiquitination at K410 (P = 0.0816);Loss of ubiquitination at K410 (P = 0.0816);Loss of ubiquitination at K410 (P = 0.0816);Loss of ubiquitination at K410 (P = 0.0816);Loss of ubiquitination at K410 (P = 0.0816);Loss of ubiquitination at K410 (P = 0.0816);Loss of ubiquitination at K410 (P = 0.0816);Loss of ubiquitination at K410 (P = 0.0816);Loss of ubiquitination at K410 (P = 0.0816);Loss of ubiquitination at K410 (P = 0.0816);Loss of ubiquitination at K410 (P = 0.0816);Loss of ubiquitination at K410 (P = 0.0816);Loss of ubiquitination at K410 (P = 0.0816);Loss of ubiquitination at K410 (P = 0.0816);
MVP		0.99
MPC		2.4
ClinPred		1.0	D
GERP RS		5.3
gMVP		0.99

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	0.97
dbscSNV1_RF	Benign	0.67
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs79891110; hg19: chr12-2614110; COSMIC: COSV100223378;