rs1279028766

Positions:

• chr12-2691116-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM2 PP2 BP4_Moderate

The NM_000719.7(CACNA1C):​c.6334G>C​(p.Glu2112Gln) variant causes a missense change. The variant allele was found at a frequency of 0.000000685 in 1,459,624 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 11/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: CACNA1C NM_000719.7 missense
• Clinical Significance: Uncertain significance criteria provided, multiple submitters, no conflicts U:2
• Conservation: PhyloP100: 4.13

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]

CACNA1C-AS1 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP2: Missense variant in gene, where missense usually causes diseases (based on misZ statistic), CACNA1C. . Gene score misZ 6.4654 (greater than the threshold 3.09). Trascript score misZ 7.2674 (greater than threshold 3.09). GenCC has associacion of gene with intellectual disability, neurodevelopmental disorder with hypotonia, language delay, and skeletal defects with or without seizures, Brugada syndrome, long QT syndrome, short QT syndrome, long qt syndrome 8, Timothy syndrome, Brugada syndrome 3.
• BP4: Computational evidence support a benign effect (MetaRNN=0.15111059).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CACNA1C	NM_000719.7	c.6334G>C	p.Glu2112Gln	missense_variant	47/47	ENST00000399655.6	NP_000710.5
CACNA1C	NM_001167623.2	c.6334G>C	p.Glu2112Gln	missense_variant	47/47	ENST00000399603.6	NP_001161095.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CACNA1C	ENST00000399603.6	c.6334G>C	p.Glu2112Gln	missense_variant	47/47	5	NM_001167623.2	ENSP00000382512.1
CACNA1C	ENST00000399655.6	c.6334G>C	p.Glu2112Gln	missense_variant	47/47	1	NM_000719.7	ENSP00000382563.1
CACNA1C	ENST00000682544.1	c.6673G>C	p.Glu2225Gln	missense_variant	50/50			ENSP00000507184.1
CACNA1C	ENST00000406454.8	c.6547G>C	p.Glu2183Gln	missense_variant	48/48	5		ENSP00000385896.3
CACNA1C	ENST00000399634.6	c.6514G>C	p.Glu2172Gln	missense_variant	47/47	5		ENSP00000382542.2
CACNA1C	ENST00000683824.1	c.6499G>C	p.Glu2167Gln	missense_variant	48/48			ENSP00000507867.1
CACNA1C	ENST00000347598.9	c.6478G>C	p.Glu2160Gln	missense_variant	49/49	1		ENSP00000266376.6
CACNA1C	ENST00000344100.7	c.6457G>C	p.Glu2153Gln	missense_variant	47/47	1		ENSP00000341092.3
CACNA1C	ENST00000327702.12	c.6439G>C	p.Glu2147Gln	missense_variant	48/48	1		ENSP00000329877.7
CACNA1C	ENST00000399617.6	c.6439G>C	p.Glu2147Gln	missense_variant	48/48	5		ENSP00000382526.1
CACNA1C	ENST00000682462.1	c.6424G>C	p.Glu2142Gln	missense_variant	47/47			ENSP00000507105.1
CACNA1C	ENST00000683781.1	c.6424G>C	p.Glu2142Gln	missense_variant	47/47			ENSP00000507434.1
CACNA1C	ENST00000683840.1	c.6424G>C	p.Glu2142Gln	missense_variant	47/47			ENSP00000507612.1
CACNA1C	ENST00000683956.1	c.6424G>C	p.Glu2142Gln	missense_variant	47/47			ENSP00000506882.1
CACNA1C	ENST00000399638.5	c.6418G>C	p.Glu2140Gln	missense_variant	48/48	1		ENSP00000382547.1
CACNA1C	ENST00000335762.10	c.6409G>C	p.Glu2137Gln	missense_variant	48/48	5		ENSP00000336982.5
CACNA1C	ENST00000399606.5	c.6394G>C	p.Glu2132Gln	missense_variant	48/48	1		ENSP00000382515.1
CACNA1C	ENST00000399621.5	c.6391G>C	p.Glu2131Gln	missense_variant	47/47	1		ENSP00000382530.1
CACNA1C	ENST00000399637.5	c.6391G>C	p.Glu2131Gln	missense_variant	47/47	1		ENSP00000382546.1
CACNA1C	ENST00000402845.7	c.6391G>C	p.Glu2131Gln	missense_variant	47/47	1		ENSP00000385724.3
CACNA1C	ENST00000399629.5	c.6385G>C	p.Glu2129Gln	missense_variant	47/47	1		ENSP00000382537.1
CACNA1C	ENST00000682336.1	c.6376G>C	p.Glu2126Gln	missense_variant	47/47			ENSP00000507898.1
CACNA1C	ENST00000399591.5	c.6358G>C	p.Glu2120Gln	missense_variant	46/46	1		ENSP00000382500.1
CACNA1C	ENST00000399595.5	c.6358G>C	p.Glu2120Gln	missense_variant	46/46	1		ENSP00000382504.1
CACNA1C	ENST00000399649.5	c.6352G>C	p.Glu2118Gln	missense_variant	46/46	1		ENSP00000382557.1
CACNA1C	ENST00000399597.5	c.6334G>C	p.Glu2112Gln	missense_variant	47/47	1		ENSP00000382506.1
CACNA1C	ENST00000399601.5	c.6334G>C	p.Glu2112Gln	missense_variant	47/47	1		ENSP00000382510.1
CACNA1C	ENST00000399641.6	c.6334G>C	p.Glu2112Gln	missense_variant	47/47	1		ENSP00000382549.1
CACNA1C	ENST00000399644.5	c.6334G>C	p.Glu2112Gln	missense_variant	47/47	1		ENSP00000382552.1
CACNA1C	ENST00000682835.1	c.6334G>C	p.Glu2112Gln	missense_variant	47/47			ENSP00000507282.1
CACNA1C	ENST00000683482.1	c.6325G>C	p.Glu2109Gln	missense_variant	47/47			ENSP00000507169.1
CACNA1C	ENST00000682686.1	c.6301G>C	p.Glu2101Gln	missense_variant	46/46			ENSP00000507309.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD3 exomes AF: 0.00000408 AC: 1 AN: 244862 Hom.: 0 AF XY: 0.00000748 AC XY: 1 AN XY: 133652

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000292

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 6.85e-7 AC: 1 AN: 1459624 Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1 AN XY: 725856

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000224

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 Cov.: 33

Bravo AF: 0.00000378

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Timothy syndrome;C2678478:Brugada syndrome 3;CN260585:Long qt syndrome 8 Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Sep 01, 2021

- -

Long QT syndrome Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 25, 2017

This variant is not present in population databases (ExAC no frequency) and has not been reported in the literature in individuals with a CACNA1C-related disease. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The glutamine amino acid residue is found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. These predictions have not been confirmed by published functional studies. In summary, this variant is a novel missense change that is not predicted to affect protein function. There is no indication that it causes disease, but the available evidence is currently insufficient to prove that conclusively. Therefore, it has been classified as a Variant of Uncertain Significance. This sequence change replaces glutamic acid with glutamine at codon 2112 of the CACNA1C protein (p.Glu2112Gln). The glutamic acid residue is weakly conserved and there is a small physicochemical difference between glutamic acid and glutamine. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.19	T
BayesDel_noAF	Benign	-0.43
CADD	Benign	23
DANN	Uncertain	0.98
DEOGEN2	Benign	0.014	T;.;.;.;.;.;.;.;.;.;.;.;.;.;.;T;.;.;.;.;T;.;T
Eigen	Benign	-0.12
Eigen_PC	Benign	-0.048
FATHMM_MKL	Uncertain	0.88	D
M_CAP	Benign	0.016	T
MetaRNN	Benign	0.15	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM	Benign	-0.95	T
PrimateAI	Uncertain	0.55	T
PROVEAN	Benign	-0.50	N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;.
REVEL	Benign	0.049
Sift	Benign	0.11	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;.
Sift4G	Benign	0.16	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
Polyphen		0.0, 0.41, 0.35, 0.55, 0.30, 0.71, 0.18, 0.40, 0.94, 0.71, 0.95, 0.0010	.;B;B;B;P;B;P;B;B;B;B;B;B;P;B;.;P;P;.;.;.;B;.
Vest4		0.19
MVP		0.67
MPC		0.19
ClinPred		0.29	T
GERP RS		3.6
gMVP		0.51

Splicing

Name	Calibrated prediction	Score	Prediction
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: rs1279028766; hg19: chr12-2800282;