12-2115224-G-T

Variant names:

• chr12-2115224-G-T
• NM_000719.7:c.50G>T

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2 PP2 PP3

The NM_000719.7(CACNA1C):​c.50G>T​(p.Gly17Val) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000712 in 1,404,104 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 34)
  • Exomes 𝑓: 7.1e-7 (0 hom.)
• Consequence: CACNA1C NM_000719.7 missense, splice_region
• Scores: Splicing: ADA: 0.9993
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 8.01

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 4 ACMG points.

• 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: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF. No scorers claiming Uncertain. Scorers claiming Benign: max_spliceai.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNA1C	NM_000719.7	c.50G>T	p.Gly17Val	missense_variant, splice_region_variant	Exon 2 of 47	ENST00000399655.6	NP_000710.5
CACNA1C	NM_001167623.2	c.50G>T	p.Gly17Val	missense_variant, splice_region_variant	Exon 2 of 47	ENST00000399603.6	NP_001161095.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CACNA1C	ENST00000399603.6	c.50G>T	p.Gly17Val	missense_variant, splice_region_variant	Exon 2 of 47	5	NM_001167623.2	ENSP00000382512.1
CACNA1C	ENST00000399655.6	c.50G>T	p.Gly17Val	missense_variant, splice_region_variant	Exon 2 of 47	1	NM_000719.7	ENSP00000382563.1
CACNA1C	ENST00000682544.1	c.140G>T	p.Gly47Val	missense_variant, splice_region_variant	Exon 2 of 50			ENSP00000507184.1
CACNA1C	ENST00000406454.8	c.50G>T	p.Gly17Val	missense_variant, splice_region_variant	Exon 2 of 48	5		ENSP00000385896.3
CACNA1C	ENST00000399634.6	c.50G>T	p.Gly17Val	missense_variant, splice_region_variant	Exon 2 of 47	5		ENSP00000382542.2
CACNA1C	ENST00000683824.1	c.140G>T	p.Gly47Val	missense_variant, splice_region_variant	Exon 2 of 48			ENSP00000507867.1
CACNA1C	ENST00000347598.9	c.50G>T	p.Gly17Val	missense_variant, splice_region_variant	Exon 2 of 49	1		ENSP00000266376.6
CACNA1C	ENST00000344100.7	c.50G>T	p.Gly17Val	missense_variant, splice_region_variant	Exon 2 of 47	1		ENSP00000341092.3
CACNA1C	ENST00000327702.12	c.50G>T	p.Gly17Val	missense_variant, splice_region_variant	Exon 2 of 48	1		ENSP00000329877.7
CACNA1C	ENST00000399617.6	c.50G>T	p.Gly17Val	missense_variant, splice_region_variant	Exon 2 of 48	5		ENSP00000382526.1
CACNA1C	ENST00000682462.1	c.140G>T	p.Gly47Val	missense_variant, splice_region_variant	Exon 2 of 47			ENSP00000507105.1
CACNA1C	ENST00000683781.1	c.140G>T	p.Gly47Val	missense_variant, splice_region_variant	Exon 2 of 47			ENSP00000507434.1
CACNA1C	ENST00000683840.1	c.140G>T	p.Gly47Val	missense_variant, splice_region_variant	Exon 2 of 47			ENSP00000507612.1
CACNA1C	ENST00000683956.1	c.140G>T	p.Gly47Val	missense_variant, splice_region_variant	Exon 2 of 47			ENSP00000506882.1
CACNA1C	ENST00000399638.5	c.50G>T	p.Gly17Val	missense_variant, splice_region_variant	Exon 2 of 48	1		ENSP00000382547.1
CACNA1C	ENST00000335762.10	c.50G>T	p.Gly17Val	missense_variant, splice_region_variant	Exon 2 of 48	5		ENSP00000336982.5
CACNA1C	ENST00000399606.5	c.50G>T	p.Gly17Val	missense_variant, splice_region_variant	Exon 2 of 48	1		ENSP00000382515.1
CACNA1C	ENST00000399621.5	c.50G>T	p.Gly17Val	missense_variant, splice_region_variant	Exon 2 of 47	1		ENSP00000382530.1
CACNA1C	ENST00000399637.5	c.50G>T	p.Gly17Val	missense_variant, splice_region_variant	Exon 2 of 47	1		ENSP00000382546.1
CACNA1C	ENST00000402845.7	c.50G>T	p.Gly17Val	missense_variant, splice_region_variant	Exon 2 of 47	1		ENSP00000385724.3
CACNA1C	ENST00000399629.5	c.50G>T	p.Gly17Val	missense_variant, splice_region_variant	Exon 2 of 47	1		ENSP00000382537.1
CACNA1C	ENST00000682336.1	c.50G>T	p.Gly17Val	missense_variant, splice_region_variant	Exon 2 of 47			ENSP00000507898.1
CACNA1C	ENST00000399591.5	c.50G>T	p.Gly17Val	missense_variant, splice_region_variant	Exon 2 of 46	1		ENSP00000382500.1
CACNA1C	ENST00000399595.5	c.50G>T	p.Gly17Val	missense_variant, splice_region_variant	Exon 2 of 46	1		ENSP00000382504.1
CACNA1C	ENST00000399649.5	c.50G>T	p.Gly17Val	missense_variant, splice_region_variant	Exon 2 of 46	1		ENSP00000382557.1
CACNA1C	ENST00000399597.5	c.50G>T	p.Gly17Val	missense_variant, splice_region_variant	Exon 2 of 47	1		ENSP00000382506.1
CACNA1C	ENST00000399601.5	c.50G>T	p.Gly17Val	missense_variant, splice_region_variant	Exon 2 of 47	1		ENSP00000382510.1
CACNA1C	ENST00000399641.6	c.50G>T	p.Gly17Val	missense_variant, splice_region_variant	Exon 2 of 47	1		ENSP00000382549.1
CACNA1C	ENST00000399644.5	c.50G>T	p.Gly17Val	missense_variant, splice_region_variant	Exon 2 of 47	1		ENSP00000382552.1
CACNA1C	ENST00000682835.1	c.50G>T	p.Gly17Val	missense_variant, splice_region_variant	Exon 2 of 47			ENSP00000507282.1
CACNA1C	ENST00000683482.1	c.50G>T	p.Gly17Val	missense_variant, splice_region_variant	Exon 2 of 47			ENSP00000507169.1
CACNA1C	ENST00000682686.1	c.50G>T	p.Gly17Val	missense_variant, splice_region_variant	Exon 2 of 46			ENSP00000507309.1
CACNA1C	ENST00000682152	c.-2G>T		5_prime_UTR_variant	Exon 1 of 6			ENSP00000506759.1
CACNA1C	ENST00000480911.6	n.50G>T		splice_region_variant, non_coding_transcript_exon_variant	Exon 2 of 27	5		ENSP00000437936.2

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome AF: 7.12e-7 AC: 1 AN: 1404104 Hom.: 0 Cov.: 31 AF XY: 0.00000145 AC XY: 1 AN XY: 691562

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000130

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.56	D
BayesDel_noAF	Pathogenic	0.56
CADD	Pathogenic	28
DANN	Uncertain	1.0
DEOGEN2	Benign	0.024	.;T;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;T;.;.;.;.;T;.
Eigen	Uncertain	0.58
Eigen_PC	Uncertain	0.64
FATHMM_MKL	Pathogenic	0.99	D
M_CAP	Pathogenic	0.78	D
MetaRNN	Pathogenic	0.83	D;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	0.93	D
PrimateAI	Uncertain	0.71	T
PROVEAN	Pathogenic	-6.9	D;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N
REVEL	Uncertain	0.63
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;D
Sift4G	Pathogenic	0.0	D;D;D;D;D;D;D;D;D;D;D;D;T;D;D;T;D;D;D;D;D;T;D;T
Polyphen		0.69, 0.14, 0.97, 0.94, 0.99, 1.0, 0.65, 1.0	.;.;P;.;B;D;P;D;D;D;P;D;D;D;D;D;D;.;D;D;.;.;.;.
Vest4		0.73, 0.77, 0.73, 0.76, 0.75, 0.74, 0.74, 0.77, 0.77, 0.78, 0.78, 0.74, 0.74, 0.77, 0.76, 0.77, 0.69, 0.74
MutPred		0.38		.;Gain of catalytic residue at Y20 (P = 0);Gain of catalytic residue at Y20 (P = 0);Gain of catalytic residue at Y20 (P = 0);Gain of catalytic residue at Y20 (P = 0);Gain of catalytic residue at Y20 (P = 0);Gain of catalytic residue at Y20 (P = 0);Gain of catalytic residue at Y20 (P = 0);Gain of catalytic residue at Y20 (P = 0);Gain of catalytic residue at Y20 (P = 0);Gain of catalytic residue at Y20 (P = 0);Gain of catalytic residue at Y20 (P = 0);Gain of catalytic residue at Y20 (P = 0);Gain of catalytic residue at Y20 (P = 0);Gain of catalytic residue at Y20 (P = 0);Gain of catalytic residue at Y20 (P = 0);Gain of catalytic residue at Y20 (P = 0);Gain of catalytic residue at Y20 (P = 0);Gain of catalytic residue at Y20 (P = 0);Gain of catalytic residue at Y20 (P = 0);Gain of catalytic residue at Y20 (P = 0);Gain of catalytic residue at Y20 (P = 0);Gain of catalytic residue at Y20 (P = 0);Gain of catalytic residue at Y20 (P = 0);
MVP		0.95
MPC		2.2
ClinPred		0.93	D
GERP RS		5.8
gMVP		0.81

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.90
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: chr12-2224390;