12-2053579-C-T

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.17C>T(p.Thr6Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000069 in 1,448,344 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T6R) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: CACNA1C NM_000719.7 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 2.44

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 Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP2: Missense variant where missense usually causes diseases, CACNA1C
• BP4: Computational evidence support a benign effect (MetaRNN=0.24788743).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CACNA1C	NM_000719.7	c.17C>T	p.Thr6Met	missense_variant	1/47	ENST00000399655.6
CACNA1C	NM_001167623.2	c.17C>T	p.Thr6Met	missense_variant	1/47	ENST00000399603.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CACNA1C	ENST00000399603.6	c.17C>T	p.Thr6Met	missense_variant	1/47	5	NM_001167623.2
CACNA1C	ENST00000399655.6	c.17C>T	p.Thr6Met	missense_variant	1/47	1	NM_000719.7

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 6.90e-7 AC: 1 AN: 1448344 Hom.: 0 Cov.: 32 AF XY: 0.00000139 AC XY: 1 AN XY: 719122

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.0000386

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.: 31

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Cardiovascular phenotype Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Apr 08, 2021

The p.T6M variant (also known as c.17C>T), located in coding exon 1 of the CACNA1C gene, results from a C to T substitution at nucleotide position 17. The threonine at codon 6 is replaced by methionine, an amino acid with similar properties. This amino acid position is well conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CardioboostArm	Benign	0.00044
BayesDel_addAF	Uncertain	0.062	T
BayesDel_noAF	Benign	-0.15
Cadd	Uncertain	25
Dann	Benign	0.97
DEOGEN2	Benign	0.0046	T;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;T;.;.;.;.;T;.
Eigen	Benign	-0.035
Eigen_PC	Benign	-0.00034
FATHMM_MKL	Benign	0.49	N
M_CAP	Pathogenic	0.80	D
MetaRNN	Benign	0.25	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM	Uncertain	0.038	D
MutationTaster	Benign	1.0	N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N
PrimateAI	Pathogenic	0.84	D
PROVEAN	Benign	-0.010	N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N
REVEL	Benign	0.28
Sift	Uncertain	0.0030	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
Sift4G	Benign	0.089	T;T;D;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
Polyphen		0.63, 0.97, 0.95, 0.86, 0.88	.;P;.;D;P;P;P;P;P;P;P;P;P;P;P;P;.;P;P;.;.;.;.
Vest4		0.23
MutPred		0.19		Gain of catalytic residue at V2 (P = 3e-04);Gain of catalytic residue at V2 (P = 3e-04);Gain of catalytic residue at V2 (P = 3e-04);Gain of catalytic residue at V2 (P = 3e-04);Gain of catalytic residue at V2 (P = 3e-04);Gain of catalytic residue at V2 (P = 3e-04);Gain of catalytic residue at V2 (P = 3e-04);Gain of catalytic residue at V2 (P = 3e-04);Gain of catalytic residue at V2 (P = 3e-04);Gain of catalytic residue at V2 (P = 3e-04);Gain of catalytic residue at V2 (P = 3e-04);Gain of catalytic residue at V2 (P = 3e-04);Gain of catalytic residue at V2 (P = 3e-04);Gain of catalytic residue at V2 (P = 3e-04);Gain of catalytic residue at V2 (P = 3e-04);Gain of catalytic residue at V2 (P = 3e-04);Gain of catalytic residue at V2 (P = 3e-04);Gain of catalytic residue at V2 (P = 3e-04);Gain of catalytic residue at V2 (P = 3e-04);Gain of catalytic residue at V2 (P = 3e-04);Gain of catalytic residue at V2 (P = 3e-04);Gain of catalytic residue at V2 (P = 3e-04);Gain of catalytic residue at V2 (P = 3e-04);
MVP		0.53
MPC		2.0
ClinPred		0.50	D
GERP RS		2.0
gMVP		0.67

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: chr12-2162745; COSMIC: COSV59712808; COSMIC: COSV59712808;