12-2605112-C-T

Variant names:

• chr12-2605112-C-T
• rs1555878994
• NM_000719.7:c.2992C>T

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1 PM2 PP5_Moderate

The NM_000719.7(CACNA1C):​c.2992C>T​(p.Arg998*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. 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 Pathogenic (★). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CACNA1C NM_000719.7 stop_gained
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 0.678

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 Pathogenic. Variant got 12 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 12-2605112-C-T is Pathogenic according to our data. Variant chr12-2605112-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 3573697.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNA1C	NM_000719.7	c.2992C>T	p.Arg998*	stop_gained	Exon 23 of 47	ENST00000399655.6	NP_000710.5
CACNA1C	NM_001167623.2	c.2992C>T	p.Arg998*	stop_gained	Exon 23 of 47	ENST00000399603.6	NP_001161095.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CACNA1C	ENST00000399603.6	c.2992C>T	p.Arg998*	stop_gained	Exon 23 of 47	5	NM_001167623.2	ENSP00000382512.1
CACNA1C	ENST00000399655.6	c.2992C>T	p.Arg998*	stop_gained	Exon 23 of 47	1	NM_000719.7	ENSP00000382563.1
CACNA1C	ENST00000682544.1	c.3142C>T	p.Arg1048*	stop_gained	Exon 24 of 50			ENSP00000507184.1
CACNA1C	ENST00000406454.8	c.2992C>T	p.Arg998*	stop_gained	Exon 23 of 48	5		ENSP00000385896.3
CACNA1C	ENST00000399634.6	c.2992C>T	p.Arg998*	stop_gained	Exon 23 of 47	5		ENSP00000382542.2
CACNA1C	ENST00000683824.1	c.3157C>T	p.Arg1053*	stop_gained	Exon 24 of 48			ENSP00000507867.1
CACNA1C	ENST00000347598.9	c.3052C>T	p.Arg1018*	stop_gained	Exon 24 of 49	1		ENSP00000266376.6
CACNA1C	ENST00000344100.7	c.2992C>T	p.Arg998*	stop_gained	Exon 23 of 47	1		ENSP00000341092.3
CACNA1C	ENST00000327702.12	c.2992C>T	p.Arg998*	stop_gained	Exon 23 of 48	1		ENSP00000329877.7
CACNA1C	ENST00000399617.6	c.2992C>T	p.Arg998*	stop_gained	Exon 23 of 48	5		ENSP00000382526.1
CACNA1C	ENST00000682462.1	c.3082C>T	p.Arg1028*	stop_gained	Exon 23 of 47			ENSP00000507105.1
CACNA1C	ENST00000683781.1	c.3082C>T	p.Arg1028*	stop_gained	Exon 23 of 47			ENSP00000507434.1
CACNA1C	ENST00000683840.1	c.3082C>T	p.Arg1028*	stop_gained	Exon 23 of 47			ENSP00000507612.1
CACNA1C	ENST00000683956.1	c.3082C>T	p.Arg1028*	stop_gained	Exon 23 of 47			ENSP00000506882.1
CACNA1C	ENST00000399638.5	c.2992C>T	p.Arg998*	stop_gained	Exon 23 of 48	1		ENSP00000382547.1
CACNA1C	ENST00000335762.10	c.3067C>T	p.Arg1023*	stop_gained	Exon 24 of 48	5		ENSP00000336982.5
CACNA1C	ENST00000399606.5	c.3052C>T	p.Arg1018*	stop_gained	Exon 24 of 48	1		ENSP00000382515.1
CACNA1C	ENST00000399621.5	c.2992C>T	p.Arg998*	stop_gained	Exon 23 of 47	1		ENSP00000382530.1
CACNA1C	ENST00000399637.5	c.2992C>T	p.Arg998*	stop_gained	Exon 23 of 47	1		ENSP00000382546.1
CACNA1C	ENST00000402845.7	c.2992C>T	p.Arg998*	stop_gained	Exon 23 of 47	1		ENSP00000385724.3
CACNA1C	ENST00000399629.5	c.2992C>T	p.Arg998*	stop_gained	Exon 23 of 47	1		ENSP00000382537.1
CACNA1C	ENST00000682336.1	c.3067C>T	p.Arg1023*	stop_gained	Exon 24 of 47			ENSP00000507898.1
CACNA1C	ENST00000399591.5	c.2992C>T	p.Arg998*	stop_gained	Exon 23 of 46	1		ENSP00000382500.1
CACNA1C	ENST00000399595.5	c.2992C>T	p.Arg998*	stop_gained	Exon 23 of 46	1		ENSP00000382504.1
CACNA1C	ENST00000399649.5	c.2992C>T	p.Arg998*	stop_gained	Exon 23 of 46	1		ENSP00000382557.1
CACNA1C	ENST00000399597.5	c.2992C>T	p.Arg998*	stop_gained	Exon 23 of 47	1		ENSP00000382506.1
CACNA1C	ENST00000399601.5	c.2992C>T	p.Arg998*	stop_gained	Exon 23 of 47	1		ENSP00000382510.1
CACNA1C	ENST00000399641.6	c.2992C>T	p.Arg998*	stop_gained	Exon 23 of 47	1		ENSP00000382549.1
CACNA1C	ENST00000399644.5	c.2992C>T	p.Arg998*	stop_gained	Exon 23 of 47	1		ENSP00000382552.1
CACNA1C	ENST00000682835.1	c.2992C>T	p.Arg998*	stop_gained	Exon 23 of 47			ENSP00000507282.1
CACNA1C	ENST00000683482.1	c.2983C>T	p.Arg995*	stop_gained	Exon 23 of 47			ENSP00000507169.1
CACNA1C	ENST00000682686.1	c.2992C>T	p.Arg998*	stop_gained	Exon 23 of 46			ENSP00000507309.1
CACNA1C	ENST00000480911.6	n.*1599C>T		non_coding_transcript_exon_variant	Exon 21 of 27	5		ENSP00000437936.2
CACNA1C	ENST00000480911.6	n.*1599C>T		3_prime_UTR_variant	Exon 21 of 27	5		ENSP00000437936.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Pathogenic:1

Jul 14, 2024

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); Has not been previously published as pathogenic or benign to our knowledge -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.63	D
BayesDel_noAF	Pathogenic	0.57
CADD	Pathogenic	37
DANN	Uncertain	1.0
Eigen	Uncertain	0.47
Eigen_PC	Uncertain	0.27
FATHMM_MKL	Uncertain	0.88	D
Vest4		0.89
GERP RS		1.1

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1555878994; hg19: chr12-2714278; COSMIC: COSV59712986; COSMIC: COSV59712986;