NM_000719.7:c.3398G>A

Variant names:

• chr12-2608552-G-A
• rs1555884489
• NM_000719.7:c.3398G>A

Variant summary

Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM1 PM2 PP2 PP3_Moderate

The NM_000719.7(CACNA1C):​c.3398G>A​(p.Gly1133Asp) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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 Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: CACNA1C NM_000719.7 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 9.60

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 Likely_pathogenic. Variant got 7 ACMG points.

• PM1: In a region_of_interest Dihydropyridine binding (size 89) in uniprot entity CAC1C_HUMAN there are 6 pathogenic changes around while only 0 benign (100%) in NM_000719.7
• PM2: Very rare variant in population databases, with high coverage
• PP2: Missense variant in the CACNA1C gene, where missense mutations are typically associated with disease (based on misZ statistic). The gene has 45 curated pathogenic missense variants (we use a threshold of 10). The gene has 91 curated benign missense variants. Gene score misZ: 6.4654 (above the threshold of 3.09). Trascript score misZ: 7.2674 (above the threshold of 3.09). GenCC associations: The gene is linked to 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.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.909

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNA1C	NM_000719.7	c.3398G>A	p.Gly1133Asp	missense_variant	Exon 27 of 47	ENST00000399655.6	NP_000710.5
CACNA1C	NM_001167623.2	c.3398G>A	p.Gly1133Asp	missense_variant	Exon 27 of 47	ENST00000399603.6	NP_001161095.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CACNA1C	ENST00000399603.6	c.3398G>A	p.Gly1133Asp	missense_variant	Exon 27 of 47	5	NM_001167623.2	ENSP00000382512.1
CACNA1C	ENST00000399655.6	c.3398G>A	p.Gly1133Asp	missense_variant	Exon 27 of 47	1	NM_000719.7	ENSP00000382563.1
CACNA1C	ENST00000682544.1	c.3548G>A	p.Gly1183Asp	missense_variant	Exon 28 of 50			ENSP00000507184.1
CACNA1C	ENST00000406454.8	c.3398G>A	p.Gly1133Asp	missense_variant	Exon 27 of 48	5		ENSP00000385896.3
CACNA1C	ENST00000399634.6	c.3398G>A	p.Gly1133Asp	missense_variant	Exon 27 of 47	5		ENSP00000382542.2
CACNA1C	ENST00000683824.1	c.3563G>A	p.Gly1188Asp	missense_variant	Exon 28 of 48			ENSP00000507867.1
CACNA1C	ENST00000347598.9	c.3458G>A	p.Gly1153Asp	missense_variant	Exon 28 of 49	1		ENSP00000266376.6
CACNA1C	ENST00000344100.7	c.3398G>A	p.Gly1133Asp	missense_variant	Exon 27 of 47	1		ENSP00000341092.3
CACNA1C	ENST00000327702.12	c.3398G>A	p.Gly1133Asp	missense_variant	Exon 27 of 48	1		ENSP00000329877.7
CACNA1C	ENST00000399617.6	c.3398G>A	p.Gly1133Asp	missense_variant	Exon 27 of 48	5		ENSP00000382526.1
CACNA1C	ENST00000682462.1	c.3488G>A	p.Gly1163Asp	missense_variant	Exon 27 of 47			ENSP00000507105.1
CACNA1C	ENST00000683781.1	c.3488G>A	p.Gly1163Asp	missense_variant	Exon 27 of 47			ENSP00000507434.1
CACNA1C	ENST00000683840.1	c.3488G>A	p.Gly1163Asp	missense_variant	Exon 27 of 47			ENSP00000507612.1
CACNA1C	ENST00000683956.1	c.3488G>A	p.Gly1163Asp	missense_variant	Exon 27 of 47			ENSP00000506882.1
CACNA1C	ENST00000399638.5	c.3398G>A	p.Gly1133Asp	missense_variant	Exon 27 of 48	1		ENSP00000382547.1
CACNA1C	ENST00000335762.10	c.3473G>A	p.Gly1158Asp	missense_variant	Exon 28 of 48	5		ENSP00000336982.5
CACNA1C	ENST00000399606.5	c.3458G>A	p.Gly1153Asp	missense_variant	Exon 28 of 48	1		ENSP00000382515.1
CACNA1C	ENST00000399621.5	c.3398G>A	p.Gly1133Asp	missense_variant	Exon 27 of 47	1		ENSP00000382530.1
CACNA1C	ENST00000399637.5	c.3398G>A	p.Gly1133Asp	missense_variant	Exon 27 of 47	1		ENSP00000382546.1
CACNA1C	ENST00000402845.7	c.3398G>A	p.Gly1133Asp	missense_variant	Exon 27 of 47	1		ENSP00000385724.3
CACNA1C	ENST00000399629.5	c.3398G>A	p.Gly1133Asp	missense_variant	Exon 27 of 47	1		ENSP00000382537.1
CACNA1C	ENST00000682336.1	c.3473G>A	p.Gly1158Asp	missense_variant	Exon 28 of 47			ENSP00000507898.1
CACNA1C	ENST00000399591.5	c.3398G>A	p.Gly1133Asp	missense_variant	Exon 27 of 46	1		ENSP00000382500.1
CACNA1C	ENST00000399595.5	c.3398G>A	p.Gly1133Asp	missense_variant	Exon 27 of 46	1		ENSP00000382504.1
CACNA1C	ENST00000399649.5	c.3398G>A	p.Gly1133Asp	missense_variant	Exon 27 of 46	1		ENSP00000382557.1
CACNA1C	ENST00000399597.5	c.3398G>A	p.Gly1133Asp	missense_variant	Exon 27 of 47	1		ENSP00000382506.1
CACNA1C	ENST00000399601.5	c.3398G>A	p.Gly1133Asp	missense_variant	Exon 27 of 47	1		ENSP00000382510.1
CACNA1C	ENST00000399641.6	c.3398G>A	p.Gly1133Asp	missense_variant	Exon 27 of 47	1		ENSP00000382549.1
CACNA1C	ENST00000399644.5	c.3398G>A	p.Gly1133Asp	missense_variant	Exon 27 of 47	1		ENSP00000382552.1
CACNA1C	ENST00000682835.1	c.3398G>A	p.Gly1133Asp	missense_variant	Exon 27 of 47			ENSP00000507282.1
CACNA1C	ENST00000683482.1	c.3389G>A	p.Gly1130Asp	missense_variant	Exon 27 of 47			ENSP00000507169.1
CACNA1C	ENST00000682686.1	c.3398G>A	p.Gly1133Asp	missense_variant	Exon 27 of 46			ENSP00000507309.1
CACNA1C	ENST00000480911.6	n.*2005G>A		non_coding_transcript_exon_variant	Exon 25 of 27	5		ENSP00000437936.2
CACNA1C	ENST00000480911.6	n.*2005G>A		3_prime_UTR_variant	Exon 25 of 27	5		ENSP00000437936.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Long QT syndrome Uncertain:1

Jun 25, 2017

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces glycine with aspartic acid at codon 1133 of the CACNA1C protein (p.Gly1133Asp). The glycine residue is highly conserved and there is a moderate physicochemical difference between glycine and aspartic acid. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with CACNA1C-related disease. Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). 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. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.56	D
BayesDel_noAF	Pathogenic	0.57
CADD	Pathogenic	29
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.70	D;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;T;.;.;.;.;T;.;.
Eigen	Pathogenic	1.0
Eigen_PC	Pathogenic	0.91
FATHMM_MKL	Pathogenic	0.99	D
M_CAP	Pathogenic	0.79	D
MetaRNN	Pathogenic	0.91	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	3.8	.;.;.;.;.;.;.;.;.;.;.;H;H;.;.;.;.;.;.;.;.;.;.;.
PrimateAI	Pathogenic	0.91	D
PROVEAN	Pathogenic	-6.6	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;.
REVEL	Pathogenic	0.94
Sift	Uncertain	0.0010	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;.
Sift4G	Pathogenic	0.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
Polyphen		1.0	.;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;.;D;D;.;.;.;D;.
Vest4		0.91
MutPred		0.54		.;.;.;.;.;.;.;.;.;.;.;Gain of catalytic residue at N1157 (P = 0.0424);Gain of catalytic residue at N1157 (P = 0.0424);.;.;.;.;.;.;.;.;.;.;.;
MVP		0.97
MPC		2.5
ClinPred		1.0	D
GERP RS		4.7
gMVP		0.99

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: rs1555884489; hg19: chr12-2717718; COSMIC: COSV59748429; COSMIC: COSV59748429;