NM_000719.7:c.1337A>G

Variant names:

• chr12-2512931-A-G
• rs1060503452
• NM_000719.7:c.1337A>G

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.1337A>G​(p.Asp446Gly) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic 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: 6.05

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 topological_domain Cytoplasmic (size 122) in uniprot entity CAC1C_HUMAN there are 9 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, 0.889

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNA1C	NM_000719.7	c.1337A>G	p.Asp446Gly	missense_variant	Exon 9 of 47	ENST00000399655.6	NP_000710.5
CACNA1C	NM_001167623.2	c.1337A>G	p.Asp446Gly	missense_variant	Exon 9 of 47	ENST00000399603.6	NP_001161095.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CACNA1C	ENST00000399603.6	c.1337A>G	p.Asp446Gly	missense_variant	Exon 9 of 47	5	NM_001167623.2	ENSP00000382512.1
CACNA1C	ENST00000399655.6	c.1337A>G	p.Asp446Gly	missense_variant	Exon 9 of 47	1	NM_000719.7	ENSP00000382563.1
CACNA1C	ENST00000682544.1	c.1427A>G	p.Asp476Gly	missense_variant	Exon 9 of 50			ENSP00000507184.1
CACNA1C	ENST00000406454.8	c.1337A>G	p.Asp446Gly	missense_variant	Exon 9 of 48	5		ENSP00000385896.3
CACNA1C	ENST00000399634.6	c.1337A>G	p.Asp446Gly	missense_variant	Exon 9 of 47	5		ENSP00000382542.2
CACNA1C	ENST00000683824.1	c.1427A>G	p.Asp476Gly	missense_variant	Exon 9 of 48			ENSP00000507867.1
CACNA1C	ENST00000347598.9	c.1337A>G	p.Asp446Gly	missense_variant	Exon 9 of 49	1		ENSP00000266376.6
CACNA1C	ENST00000344100.7	c.1337A>G	p.Asp446Gly	missense_variant	Exon 9 of 47	1		ENSP00000341092.3
CACNA1C	ENST00000327702.12	c.1337A>G	p.Asp446Gly	missense_variant	Exon 9 of 48	1		ENSP00000329877.7
CACNA1C	ENST00000399617.6	c.1337A>G	p.Asp446Gly	missense_variant	Exon 9 of 48	5		ENSP00000382526.1
CACNA1C	ENST00000682462.1	c.1427A>G	p.Asp476Gly	missense_variant	Exon 9 of 47			ENSP00000507105.1
CACNA1C	ENST00000683781.1	c.1427A>G	p.Asp476Gly	missense_variant	Exon 9 of 47			ENSP00000507434.1
CACNA1C	ENST00000683840.1	c.1427A>G	p.Asp476Gly	missense_variant	Exon 9 of 47			ENSP00000507612.1
CACNA1C	ENST00000683956.1	c.1427A>G	p.Asp476Gly	missense_variant	Exon 9 of 47			ENSP00000506882.1
CACNA1C	ENST00000399638.5	c.1337A>G	p.Asp446Gly	missense_variant	Exon 9 of 48	1		ENSP00000382547.1
CACNA1C	ENST00000335762.10	c.1337A>G	p.Asp446Gly	missense_variant	Exon 9 of 48	5		ENSP00000336982.5
CACNA1C	ENST00000399606.5	c.1337A>G	p.Asp446Gly	missense_variant	Exon 9 of 48	1		ENSP00000382515.1
CACNA1C	ENST00000399621.5	c.1337A>G	p.Asp446Gly	missense_variant	Exon 9 of 47	1		ENSP00000382530.1
CACNA1C	ENST00000399637.5	c.1337A>G	p.Asp446Gly	missense_variant	Exon 9 of 47	1		ENSP00000382546.1
CACNA1C	ENST00000402845.7	c.1337A>G	p.Asp446Gly	missense_variant	Exon 9 of 47	1		ENSP00000385724.3
CACNA1C	ENST00000399629.5	c.1337A>G	p.Asp446Gly	missense_variant	Exon 9 of 47	1		ENSP00000382537.1
CACNA1C	ENST00000682336.1	c.1337A>G	p.Asp446Gly	missense_variant	Exon 9 of 47			ENSP00000507898.1
CACNA1C	ENST00000399591.5	c.1337A>G	p.Asp446Gly	missense_variant	Exon 9 of 46	1		ENSP00000382500.1
CACNA1C	ENST00000399595.5	c.1337A>G	p.Asp446Gly	missense_variant	Exon 9 of 46	1		ENSP00000382504.1
CACNA1C	ENST00000399649.5	c.1337A>G	p.Asp446Gly	missense_variant	Exon 9 of 46	1		ENSP00000382557.1
CACNA1C	ENST00000399597.5	c.1337A>G	p.Asp446Gly	missense_variant	Exon 9 of 47	1		ENSP00000382506.1
CACNA1C	ENST00000399601.5	c.1337A>G	p.Asp446Gly	missense_variant	Exon 9 of 47	1		ENSP00000382510.1
CACNA1C	ENST00000399641.6	c.1337A>G	p.Asp446Gly	missense_variant	Exon 9 of 47	1		ENSP00000382549.1
CACNA1C	ENST00000399644.5	c.1337A>G	p.Asp446Gly	missense_variant	Exon 9 of 47	1		ENSP00000382552.1
CACNA1C	ENST00000682835.1	c.1337A>G	p.Asp446Gly	missense_variant	Exon 9 of 47			ENSP00000507282.1
CACNA1C	ENST00000683482.1	c.1328A>G	p.Asp443Gly	missense_variant	Exon 9 of 47			ENSP00000507169.1
CACNA1C	ENST00000682686.1	c.1337A>G	p.Asp446Gly	missense_variant	Exon 9 of 46			ENSP00000507309.1
CACNA1C	ENST00000480911.6	n.1113+19545A>G		intron_variant	Intron 7 of 26	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

Apr 07, 2016

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

In summary, this variant is a novel missense change with uncertain impact on protein function. It has been classified as a Variant of Uncertain Significance. 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"). 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. This sequence change replaces aspartic acid with glycine at codon 446 of the CACNA1C protein (p.Asp446Gly). The aspartic acid residue is highly conserved and there is a moderate physicochemical difference between aspartic acid and glycine. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.47	D
BayesDel_noAF	Pathogenic	0.44
CADD	Pathogenic	28
DANN	Uncertain	1.0
DEOGEN2	Benign	0.080	T;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;T;.;.;.;.;T;.
Eigen	Pathogenic	0.84
Eigen_PC	Pathogenic	0.74
FATHMM_MKL	Pathogenic	0.99	D
M_CAP	Pathogenic	0.70	D
MetaRNN	Pathogenic	0.89	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	3.7	.;H;.;H;H;H;H;H;H;H;H;H;H;H;H;H;.;H;H;H;.;.;.
PrimateAI	Pathogenic	0.83	D
PROVEAN	Pathogenic	-5.3	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	0.88
Sift	Uncertain	0.0020	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
Sift4G	Uncertain	0.0040	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, 1.0, 0.91, 1.0	.;D;.;D;D;P;D;D;D;D;D;D;D;D;D;D;.;D;D;.;.;.;D
Vest4		0.71
MutPred		0.30		Gain of catalytic residue at P449 (P = 0.0057);Gain of catalytic residue at P449 (P = 0.0057);Gain of catalytic residue at P449 (P = 0.0057);Gain of catalytic residue at P449 (P = 0.0057);Gain of catalytic residue at P449 (P = 0.0057);Gain of catalytic residue at P449 (P = 0.0057);Gain of catalytic residue at P449 (P = 0.0057);Gain of catalytic residue at P449 (P = 0.0057);Gain of catalytic residue at P449 (P = 0.0057);Gain of catalytic residue at P449 (P = 0.0057);Gain of catalytic residue at P449 (P = 0.0057);Gain of catalytic residue at P449 (P = 0.0057);Gain of catalytic residue at P449 (P = 0.0057);Gain of catalytic residue at P449 (P = 0.0057);Gain of catalytic residue at P449 (P = 0.0057);Gain of catalytic residue at P449 (P = 0.0057);Gain of catalytic residue at P449 (P = 0.0057);Gain of catalytic residue at P449 (P = 0.0057);Gain of catalytic residue at P449 (P = 0.0057);Gain of catalytic residue at P449 (P = 0.0057);Gain of catalytic residue at P449 (P = 0.0057);Gain of catalytic residue at P449 (P = 0.0057);Gain of catalytic residue at P449 (P = 0.0057);
MVP		0.93
MPC		2.5
ClinPred		1.0	D
GERP RS		4.4
gMVP		0.91

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: rs1060503452; hg19: chr12-2622097;