12-2605140-G-C

Position:

• chr12-2605140-G-C

Variant summary

Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2 PP2 PP3_Strong

The NM_000719.7(CACNA1C):​c.3020G>C​(p.Arg1007Thr) 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: 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]

CACNA1C-AS3 (HGNC:40117): (CACNA1C antisense RNA 3)

ACMG classification

Verdict is Likely_pathogenic. Variant got 7 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). The gene has 45 curated pathogenic missense variants (we use a threshold of 10). The gene has 91 curated benign missense variants. GenCC has associacion of the 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.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.97

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CACNA1C	NM_000719.7	c.3020G>C	p.Arg1007Thr	missense_variant	23/47	ENST00000399655.6	NP_000710.5
CACNA1C	NM_001167623.2	c.3020G>C	p.Arg1007Thr	missense_variant	23/47	ENST00000399603.6	NP_001161095.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CACNA1C	ENST00000399603.6	c.3020G>C	p.Arg1007Thr	missense_variant	23/47	5	NM_001167623.2	ENSP00000382512.1
CACNA1C	ENST00000399655.6	c.3020G>C	p.Arg1007Thr	missense_variant	23/47	1	NM_000719.7	ENSP00000382563.1
CACNA1C	ENST00000682544.1	c.3170G>C	p.Arg1057Thr	missense_variant	24/50			ENSP00000507184.1
CACNA1C	ENST00000406454.8	c.3020G>C	p.Arg1007Thr	missense_variant	23/48	5		ENSP00000385896.3
CACNA1C	ENST00000399634.6	c.3020G>C	p.Arg1007Thr	missense_variant	23/47	5		ENSP00000382542.2
CACNA1C	ENST00000683824.1	c.3185G>C	p.Arg1062Thr	missense_variant	24/48			ENSP00000507867.1
CACNA1C	ENST00000347598.9	c.3080G>C	p.Arg1027Thr	missense_variant	24/49	1		ENSP00000266376.6
CACNA1C	ENST00000344100.7	c.3020G>C	p.Arg1007Thr	missense_variant	23/47	1		ENSP00000341092.3
CACNA1C	ENST00000327702.12	c.3020G>C	p.Arg1007Thr	missense_variant	23/48	1		ENSP00000329877.7
CACNA1C	ENST00000399617.6	c.3020G>C	p.Arg1007Thr	missense_variant	23/48	5		ENSP00000382526.1
CACNA1C	ENST00000682462.1	c.3110G>C	p.Arg1037Thr	missense_variant	23/47			ENSP00000507105.1
CACNA1C	ENST00000683781.1	c.3110G>C	p.Arg1037Thr	missense_variant	23/47			ENSP00000507434.1
CACNA1C	ENST00000683840.1	c.3110G>C	p.Arg1037Thr	missense_variant	23/47			ENSP00000507612.1
CACNA1C	ENST00000683956.1	c.3110G>C	p.Arg1037Thr	missense_variant	23/47			ENSP00000506882.1
CACNA1C	ENST00000399638.5	c.3020G>C	p.Arg1007Thr	missense_variant	23/48	1		ENSP00000382547.1
CACNA1C	ENST00000335762.10	c.3095G>C	p.Arg1032Thr	missense_variant	24/48	5		ENSP00000336982.5
CACNA1C	ENST00000399606.5	c.3080G>C	p.Arg1027Thr	missense_variant	24/48	1		ENSP00000382515.1
CACNA1C	ENST00000399621.5	c.3020G>C	p.Arg1007Thr	missense_variant	23/47	1		ENSP00000382530.1
CACNA1C	ENST00000399637.5	c.3020G>C	p.Arg1007Thr	missense_variant	23/47	1		ENSP00000382546.1
CACNA1C	ENST00000402845.7	c.3020G>C	p.Arg1007Thr	missense_variant	23/47	1		ENSP00000385724.3
CACNA1C	ENST00000399629.5	c.3020G>C	p.Arg1007Thr	missense_variant	23/47	1		ENSP00000382537.1
CACNA1C	ENST00000682336.1	c.3095G>C	p.Arg1032Thr	missense_variant	24/47			ENSP00000507898.1
CACNA1C	ENST00000399591.5	c.3020G>C	p.Arg1007Thr	missense_variant	23/46	1		ENSP00000382500.1
CACNA1C	ENST00000399595.5	c.3020G>C	p.Arg1007Thr	missense_variant	23/46	1		ENSP00000382504.1
CACNA1C	ENST00000399649.5	c.3020G>C	p.Arg1007Thr	missense_variant	23/46	1		ENSP00000382557.1
CACNA1C	ENST00000399597.5	c.3020G>C	p.Arg1007Thr	missense_variant	23/47	1		ENSP00000382506.1
CACNA1C	ENST00000399601.5	c.3020G>C	p.Arg1007Thr	missense_variant	23/47	1		ENSP00000382510.1
CACNA1C	ENST00000399641.6	c.3020G>C	p.Arg1007Thr	missense_variant	23/47	1		ENSP00000382549.1
CACNA1C	ENST00000399644.5	c.3020G>C	p.Arg1007Thr	missense_variant	23/47	1		ENSP00000382552.1
CACNA1C	ENST00000682835.1	c.3020G>C	p.Arg1007Thr	missense_variant	23/47			ENSP00000507282.1
CACNA1C	ENST00000683482.1	c.3011G>C	p.Arg1004Thr	missense_variant	23/47			ENSP00000507169.1
CACNA1C	ENST00000682686.1	c.3020G>C	p.Arg1007Thr	missense_variant	23/46			ENSP00000507309.1
CACNA1C	ENST00000480911.6	n.*1627G>C		non_coding_transcript_exon_variant	21/27	5		ENSP00000437936.2
CACNA1C	ENST00000480911.6	n.*1627G>C		3_prime_UTR_variant	21/27	5		ENSP00000437936.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Revvity Omics, Revvity

Jul 25, 2023

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.57	D
BayesDel_noAF	Pathogenic	0.59
CADD	Pathogenic	31
DANN	Uncertain	0.99
DEOGEN2	Pathogenic	0.88	D;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;T;.;.;.;.;T;.
Eigen	Pathogenic	1.1
Eigen_PC	Pathogenic	0.94
FATHMM_MKL	Pathogenic	0.99	D
M_CAP	Pathogenic	0.92	D
MetaRNN	Pathogenic	0.97	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	1.0	D
MutationAssessor	Pathogenic	4.4	.;.;.;.;.;.;.;.;.;.;.;H;H;.;.;.;.;.;.;.;.;.;.
PrimateAI	Pathogenic	0.89	D
PROVEAN	Pathogenic	-5.8	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	0.96
Sift	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
Sift4G	Pathogenic	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
Polyphen		1.0, 0.98, 1.0, 1.0, 1.0, 0.99, 0.99	.;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;.;D;D;.;.;.;D
Vest4		0.95
MutPred		0.82		.;.;.;.;.;.;.;.;.;.;.;Loss of methylation at R1027 (P = 0.0183);Loss of methylation at R1027 (P = 0.0183);.;.;.;.;.;.;.;.;.;.;
MVP		1.0
MPC		2.6
ClinPred		1.0	D
GERP RS		4.5
gMVP		1.0

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr12-2714306;