rs1555825533

Variant names:

• chr12-2581684-A-G
• rs1555825533
• NM_000719.7:c.1990A>G

Variant summary

Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM1 PM2 PP2

The NM_000719.7(CACNA1C):​c.1990A>G​(p.Ile664Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 29)
• Consequence: CACNA1C NM_000719.7 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 7.46

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 5 ACMG points.

• PM1: In a repeat II (size 246) in uniprot entity CAC1C_HUMAN there are 13 pathogenic changes around while only 1 benign (93%) in NM_000719.7
• 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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNA1C	NM_000719.7	c.1990A>G	p.Ile664Val	missense_variant	Exon 14 of 47	ENST00000399655.6	NP_000710.5
CACNA1C	NM_001167623.2	c.1990A>G	p.Ile664Val	missense_variant	Exon 14 of 47	ENST00000399603.6	NP_001161095.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CACNA1C	ENST00000399603.6	c.1990A>G	p.Ile664Val	missense_variant	Exon 14 of 47	5	NM_001167623.2	ENSP00000382512.1
CACNA1C	ENST00000399655.6	c.1990A>G	p.Ile664Val	missense_variant	Exon 14 of 47	1	NM_000719.7	ENSP00000382563.1
CACNA1C	ENST00000682544.1	c.2080A>G	p.Ile694Val	missense_variant	Exon 14 of 50			ENSP00000507184.1
CACNA1C	ENST00000406454.8	c.1990A>G	p.Ile664Val	missense_variant	Exon 14 of 48	5		ENSP00000385896.3
CACNA1C	ENST00000399634.6	c.1990A>G	p.Ile664Val	missense_variant	Exon 14 of 47	5		ENSP00000382542.2
CACNA1C	ENST00000683824.1	c.2155A>G	p.Ile719Val	missense_variant	Exon 15 of 48			ENSP00000507867.1
CACNA1C	ENST00000347598.9	c.1990A>G	p.Ile664Val	missense_variant	Exon 14 of 49	1		ENSP00000266376.6
CACNA1C	ENST00000344100.7	c.1990A>G	p.Ile664Val	missense_variant	Exon 14 of 47	1		ENSP00000341092.3
CACNA1C	ENST00000327702.12	c.1990A>G	p.Ile664Val	missense_variant	Exon 14 of 48	1		ENSP00000329877.7
CACNA1C	ENST00000399617.6	c.1990A>G	p.Ile664Val	missense_variant	Exon 14 of 48	5		ENSP00000382526.1
CACNA1C	ENST00000682462.1	c.2080A>G	p.Ile694Val	missense_variant	Exon 14 of 47			ENSP00000507105.1
CACNA1C	ENST00000683781.1	c.2080A>G	p.Ile694Val	missense_variant	Exon 14 of 47			ENSP00000507434.1
CACNA1C	ENST00000683840.1	c.2080A>G	p.Ile694Val	missense_variant	Exon 14 of 47			ENSP00000507612.1
CACNA1C	ENST00000683956.1	c.2080A>G	p.Ile694Val	missense_variant	Exon 14 of 47			ENSP00000506882.1
CACNA1C	ENST00000399638.5	c.1990A>G	p.Ile664Val	missense_variant	Exon 14 of 48	1		ENSP00000382547.1
CACNA1C	ENST00000335762.10	c.2065A>G	p.Ile689Val	missense_variant	Exon 15 of 48	5		ENSP00000336982.5
CACNA1C	ENST00000399606.5	c.1990A>G	p.Ile664Val	missense_variant	Exon 14 of 48	1		ENSP00000382515.1
CACNA1C	ENST00000399621.5	c.1990A>G	p.Ile664Val	missense_variant	Exon 14 of 47	1		ENSP00000382530.1
CACNA1C	ENST00000399637.5	c.1990A>G	p.Ile664Val	missense_variant	Exon 14 of 47	1		ENSP00000382546.1
CACNA1C	ENST00000402845.7	c.1990A>G	p.Ile664Val	missense_variant	Exon 14 of 47	1		ENSP00000385724.3
CACNA1C	ENST00000399629.5	c.1990A>G	p.Ile664Val	missense_variant	Exon 14 of 47	1		ENSP00000382537.1
CACNA1C	ENST00000682336.1	c.2065A>G	p.Ile689Val	missense_variant	Exon 15 of 47			ENSP00000507898.1
CACNA1C	ENST00000399591.5	c.1990A>G	p.Ile664Val	missense_variant	Exon 14 of 46	1		ENSP00000382500.1
CACNA1C	ENST00000399595.5	c.1990A>G	p.Ile664Val	missense_variant	Exon 14 of 46	1		ENSP00000382504.1
CACNA1C	ENST00000399649.5	c.1990A>G	p.Ile664Val	missense_variant	Exon 14 of 46	1		ENSP00000382557.1
CACNA1C	ENST00000399597.5	c.1990A>G	p.Ile664Val	missense_variant	Exon 14 of 47	1		ENSP00000382506.1
CACNA1C	ENST00000399601.5	c.1990A>G	p.Ile664Val	missense_variant	Exon 14 of 47	1		ENSP00000382510.1
CACNA1C	ENST00000399641.6	c.1990A>G	p.Ile664Val	missense_variant	Exon 14 of 47	1		ENSP00000382549.1
CACNA1C	ENST00000399644.5	c.1990A>G	p.Ile664Val	missense_variant	Exon 14 of 47	1		ENSP00000382552.1
CACNA1C	ENST00000682835.1	c.1990A>G	p.Ile664Val	missense_variant	Exon 14 of 47			ENSP00000507282.1
CACNA1C	ENST00000683482.1	c.1981A>G	p.Ile661Val	missense_variant	Exon 14 of 47			ENSP00000507169.1
CACNA1C	ENST00000682686.1	c.1990A>G	p.Ile664Val	missense_variant	Exon 14 of 46			ENSP00000507309.1
CACNA1C	ENST00000480911.6	n.*597A>G		non_coding_transcript_exon_variant	Exon 12 of 27	5		ENSP00000437936.2
CACNA1C	ENST00000480911.6	n.*597A>G		3_prime_UTR_variant	Exon 12 of 27	5		ENSP00000437936.2

Frequencies

GnomAD3 genomes Cov.: 29

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 29

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Inborn genetic diseases Uncertain:1

Nov 04, 2016

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.31	D
BayesDel_noAF	Pathogenic	0.21
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.42	T;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;T;.;.;.;.;T;.
Eigen	Benign	0.11
Eigen_PC	Uncertain	0.23
FATHMM_MKL	Pathogenic	0.97	D
M_CAP	Pathogenic	0.30	D
MetaRNN	Uncertain	0.51	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	1.1	D
MutationAssessor	Benign	1.8	.;L;.;L;L;L;L;L;L;L;L;L;L;L;L;L;.;L;L;L;.;.;.
PrimateAI	Pathogenic	0.88	D
PROVEAN	Benign	-0.94	N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N
REVEL	Pathogenic	0.73
Sift	Uncertain	0.021	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	0.29	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
Polyphen		0.0020, 0.12, 0.36, 0.032, 0.0030, 0.0040, 0.0, 0.0060, 0.015	.;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;.;B;B;.;.;.;B
Vest4		0.54
MutPred		0.64		.;Gain of catalytic residue at L667 (P = 9e-04);Gain of catalytic residue at L667 (P = 9e-04);Gain of catalytic residue at L667 (P = 9e-04);Gain of catalytic residue at L667 (P = 9e-04);Gain of catalytic residue at L667 (P = 9e-04);Gain of catalytic residue at L667 (P = 9e-04);Gain of catalytic residue at L667 (P = 9e-04);Gain of catalytic residue at L667 (P = 9e-04);Gain of catalytic residue at L667 (P = 9e-04);Gain of catalytic residue at L667 (P = 9e-04);Gain of catalytic residue at L667 (P = 9e-04);Gain of catalytic residue at L667 (P = 9e-04);Gain of catalytic residue at L667 (P = 9e-04);Gain of catalytic residue at L667 (P = 9e-04);Gain of catalytic residue at L667 (P = 9e-04);Gain of catalytic residue at L667 (P = 9e-04);Gain of catalytic residue at L667 (P = 9e-04);Gain of catalytic residue at L667 (P = 9e-04);Gain of catalytic residue at L667 (P = 9e-04);Gain of catalytic residue at L667 (P = 9e-04);Gain of catalytic residue at L667 (P = 9e-04);Gain of catalytic residue at L667 (P = 9e-04);
MVP		0.96
MPC		1.1
ClinPred		0.98	D
GERP RS		4.4
gMVP		0.94

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: rs1555825533; hg19: chr12-2690850;