12-2664928-C-T

Position:

• chr12-2664928-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.4336C>T​(p.Pro1446Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,778 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 6.8e-7 (0 hom.)
• Consequence: CACNA1C NM_000719.7 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.774

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 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.
• BP4: Computational evidence support a benign effect (MetaRNN=0.21540222).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CACNA1C	NM_000719.7	c.4336C>T	p.Pro1446Ser	missense_variant	35/47	ENST00000399655.6	NP_000710.5
CACNA1C	NM_001167623.2	c.4336C>T	p.Pro1446Ser	missense_variant	35/47	ENST00000399603.6	NP_001161095.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CACNA1C	ENST00000399603.6	c.4336C>T	p.Pro1446Ser	missense_variant	35/47	5	NM_001167623.2	ENSP00000382512.1
CACNA1C	ENST00000399655.6	c.4336C>T	p.Pro1446Ser	missense_variant	35/47	1	NM_000719.7	ENSP00000382563.1
CACNA1C	ENST00000682544.1	c.4570C>T	p.Pro1524Ser	missense_variant	37/50			ENSP00000507184.1
CACNA1C	ENST00000406454.8	c.4336C>T	p.Pro1446Ser	missense_variant	35/48	5		ENSP00000385896.3
CACNA1C	ENST00000399634.6	c.4303C>T	p.Pro1435Ser	missense_variant	34/47	5		ENSP00000382542.2
CACNA1C	ENST00000683824.1	c.4501C>T	p.Pro1501Ser	missense_variant	36/48			ENSP00000507867.1
CACNA1C	ENST00000347598.9	c.4480C>T	p.Pro1494Ser	missense_variant	37/49	1		ENSP00000266376.6
CACNA1C	ENST00000344100.7	c.4402C>T	p.Pro1468Ser	missense_variant	35/47	1		ENSP00000341092.3
CACNA1C	ENST00000327702.12	c.4336C>T	p.Pro1446Ser	missense_variant	35/48	1		ENSP00000329877.7
CACNA1C	ENST00000399617.6	c.4336C>T	p.Pro1446Ser	missense_variant	35/48	5		ENSP00000382526.1
CACNA1C	ENST00000682462.1	c.4426C>T	p.Pro1476Ser	missense_variant	35/47			ENSP00000507105.1
CACNA1C	ENST00000683781.1	c.4426C>T	p.Pro1476Ser	missense_variant	35/47			ENSP00000507434.1
CACNA1C	ENST00000683840.1	c.4426C>T	p.Pro1476Ser	missense_variant	35/47			ENSP00000507612.1
CACNA1C	ENST00000683956.1	c.4426C>T	p.Pro1476Ser	missense_variant	35/47			ENSP00000506882.1
CACNA1C	ENST00000399638.5	c.4420C>T	p.Pro1474Ser	missense_variant	36/48	1		ENSP00000382547.1
CACNA1C	ENST00000335762.10	c.4411C>T	p.Pro1471Ser	missense_variant	36/48	5		ENSP00000336982.5
CACNA1C	ENST00000399606.5	c.4396C>T	p.Pro1466Ser	missense_variant	36/48	1		ENSP00000382515.1
CACNA1C	ENST00000399621.5	c.4336C>T	p.Pro1446Ser	missense_variant	35/47	1		ENSP00000382530.1
CACNA1C	ENST00000399637.5	c.4336C>T	p.Pro1446Ser	missense_variant	35/47	1		ENSP00000382546.1
CACNA1C	ENST00000402845.7	c.4336C>T	p.Pro1446Ser	missense_variant	35/47	1		ENSP00000385724.3
CACNA1C	ENST00000399629.5	c.4387C>T	p.Pro1463Ser	missense_variant	35/47	1		ENSP00000382537.1
CACNA1C	ENST00000682336.1	c.4378C>T	p.Pro1460Ser	missense_variant	35/47			ENSP00000507898.1
CACNA1C	ENST00000399591.5	c.4303C>T	p.Pro1435Ser	missense_variant	34/46	1		ENSP00000382500.1
CACNA1C	ENST00000399595.5	c.4303C>T	p.Pro1435Ser	missense_variant	34/46	1		ENSP00000382504.1
CACNA1C	ENST00000399649.5	c.4297C>T	p.Pro1433Ser	missense_variant	34/46	1		ENSP00000382557.1
CACNA1C	ENST00000399597.5	c.4336C>T	p.Pro1446Ser	missense_variant	35/47	1		ENSP00000382506.1
CACNA1C	ENST00000399601.5	c.4336C>T	p.Pro1446Ser	missense_variant	35/47	1		ENSP00000382510.1
CACNA1C	ENST00000399641.6	c.4336C>T	p.Pro1446Ser	missense_variant	35/47	1		ENSP00000382549.1
CACNA1C	ENST00000399644.5	c.4336C>T	p.Pro1446Ser	missense_variant	35/47	1		ENSP00000382552.1
CACNA1C	ENST00000682835.1	c.4336C>T	p.Pro1446Ser	missense_variant	35/47			ENSP00000507282.1
CACNA1C	ENST00000683482.1	c.4327C>T	p.Pro1443Ser	missense_variant	35/47			ENSP00000507169.1
CACNA1C	ENST00000682686.1	c.4303C>T	p.Pro1435Ser	missense_variant	34/46			ENSP00000507309.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD3 exomes AF: 0.00000400 AC: 1 AN: 250232 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 135532

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.0000290

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 6.84e-7 AC: 1 AN: 1461778 Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0 AN XY: 727172

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.0000224

Gnomad4 ASJ exome AF: 0.00

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.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Benign	-0.040	T
BayesDel_noAF	Benign	-0.21
CADD	Benign	18
DANN	Benign	0.94
DEOGEN2	Benign	0.28	T;.;.;.;.;.;.;.;.;.;.;.;.;.;.;T;.;.;.;.;T;.;T
Eigen	Benign	-0.78
Eigen_PC	Benign	-0.63
FATHMM_MKL	Benign	0.40	N
M_CAP	Uncertain	0.28	D
MetaRNN	Benign	0.22	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	0.060	D
MutationAssessor	Benign	-0.73	.;.;.;.;.;.;.;.;.;.;N;.;.;.;.;.;.;.;.;.;.;.;.
PrimateAI	Benign	0.43	T
PROVEAN	Benign	-0.75	N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;.
REVEL	Uncertain	0.32
Sift	Benign	0.37	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;.
Sift4G	Benign	0.37	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
Polyphen		0.0, 0.0010, 0.22, 0.018	.;B;B;B;B;B;B;B;B;B;B;B;B;B;B;.;B;B;.;.;.;B;.
Vest4		0.14
MutPred		0.48		.;.;.;.;.;.;.;.;.;.;Gain of catalytic residue at S1497 (P = 0);.;.;.;.;.;.;.;.;.;.;.;.;
MVP		0.55
MPC		1.1
ClinPred		0.069	T
GERP RS		3.2
gMVP		0.72

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: rs758143691; hg19: chr12-2774094;