chr12-2595894-G-A

Position:

• chr12-2595894-G-A

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 1P and 5B. PP2 BP6 BS2

The NM_000719.7(CACNA1C):​c.2684G>A​(p.Arg895His) variant causes a missense change. The variant allele was found at a frequency of 0.00000684 in 1,461,032 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000068 (0 hom.)
• Consequence: CACNA1C NM_000719.7 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:2 B:1
• Conservation: PhyloP100: 5.09

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 Likely_benign. Variant got -4 ACMG points.

• 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). GenCC has associacion of 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.
• BP6: Variant 12-2595894-G-A is Benign according to our data. Variant chr12-2595894-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 190656.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=1, Uncertain_significance=2}.
• BS2: High AC in GnomAdExome4 at 10 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CACNA1C	NM_000719.7	c.2684G>A	p.Arg895His	missense_variant	20/47	ENST00000399655.6	NP_000710.5
CACNA1C	NM_001167623.2	c.2684G>A	p.Arg895His	missense_variant	20/47	ENST00000399603.6	NP_001161095.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CACNA1C	ENST00000399603.6	c.2684G>A	p.Arg895His	missense_variant	20/47	5	NM_001167623.2	ENSP00000382512.1
CACNA1C	ENST00000399655.6	c.2684G>A	p.Arg895His	missense_variant	20/47	1	NM_000719.7	ENSP00000382563.1
CACNA1C	ENST00000682544.1	c.2774G>A	p.Arg925His	missense_variant	20/50			ENSP00000507184.1
CACNA1C	ENST00000406454.8	c.2684G>A	p.Arg895His	missense_variant	20/48	5		ENSP00000385896.3
CACNA1C	ENST00000399634.6	c.2684G>A	p.Arg895His	missense_variant	20/47	5		ENSP00000382542.2
CACNA1C	ENST00000683824.1	c.2849G>A	p.Arg950His	missense_variant	21/48			ENSP00000507867.1
CACNA1C	ENST00000347598.9	c.2684G>A	p.Arg895His	missense_variant	20/49	1		ENSP00000266376.6
CACNA1C	ENST00000344100.7	c.2684G>A	p.Arg895His	missense_variant	20/47	1		ENSP00000341092.3
CACNA1C	ENST00000327702.12	c.2684G>A	p.Arg895His	missense_variant	20/48	1		ENSP00000329877.7
CACNA1C	ENST00000399617.6	c.2684G>A	p.Arg895His	missense_variant	20/48	5		ENSP00000382526.1
CACNA1C	ENST00000682462.1	c.2774G>A	p.Arg925His	missense_variant	20/47			ENSP00000507105.1
CACNA1C	ENST00000683781.1	c.2774G>A	p.Arg925His	missense_variant	20/47			ENSP00000507434.1
CACNA1C	ENST00000683840.1	c.2774G>A	p.Arg925His	missense_variant	20/47			ENSP00000507612.1
CACNA1C	ENST00000683956.1	c.2774G>A	p.Arg925His	missense_variant	20/47			ENSP00000506882.1
CACNA1C	ENST00000399638.5	c.2684G>A	p.Arg895His	missense_variant	20/48	1		ENSP00000382547.1
CACNA1C	ENST00000335762.10	c.2759G>A	p.Arg920His	missense_variant	21/48	5		ENSP00000336982.5
CACNA1C	ENST00000399606.5	c.2684G>A	p.Arg895His	missense_variant	20/48	1		ENSP00000382515.1
CACNA1C	ENST00000399621.5	c.2684G>A	p.Arg895His	missense_variant	20/47	1		ENSP00000382530.1
CACNA1C	ENST00000399637.5	c.2684G>A	p.Arg895His	missense_variant	20/47	1		ENSP00000382546.1
CACNA1C	ENST00000402845.7	c.2684G>A	p.Arg895His	missense_variant	20/47	1		ENSP00000385724.3
CACNA1C	ENST00000399629.5	c.2684G>A	p.Arg895His	missense_variant	20/47	1		ENSP00000382537.1
CACNA1C	ENST00000682336.1	c.2759G>A	p.Arg920His	missense_variant	21/47			ENSP00000507898.1
CACNA1C	ENST00000399591.5	c.2684G>A	p.Arg895His	missense_variant	20/46	1		ENSP00000382500.1
CACNA1C	ENST00000399595.5	c.2684G>A	p.Arg895His	missense_variant	20/46	1		ENSP00000382504.1
CACNA1C	ENST00000399649.5	c.2684G>A	p.Arg895His	missense_variant	20/46	1		ENSP00000382557.1
CACNA1C	ENST00000399597.5	c.2684G>A	p.Arg895His	missense_variant	20/47	1		ENSP00000382506.1
CACNA1C	ENST00000399601.5	c.2684G>A	p.Arg895His	missense_variant	20/47	1		ENSP00000382510.1
CACNA1C	ENST00000399641.6	c.2684G>A	p.Arg895His	missense_variant	20/47	1		ENSP00000382549.1
CACNA1C	ENST00000399644.5	c.2684G>A	p.Arg895His	missense_variant	20/47	1		ENSP00000382552.1
CACNA1C	ENST00000682835.1	c.2684G>A	p.Arg895His	missense_variant	20/47			ENSP00000507282.1
CACNA1C	ENST00000683482.1	c.2675G>A	p.Arg892His	missense_variant	20/47			ENSP00000507169.1
CACNA1C	ENST00000682686.1	c.2684G>A	p.Arg895His	missense_variant	20/46			ENSP00000507309.1
CACNA1C	ENST00000480911.6	n.*1291G>A		non_coding_transcript_exon_variant	18/27	5		ENSP00000437936.2
CACNA1C	ENST00000480911.6	n.*1291G>A		3_prime_UTR_variant	18/27	5		ENSP00000437936.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000684 AC: 10 AN: 1461032 Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7 AN XY: 726848

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: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000720

Gnomad4 OTH exome AF: 0.0000166

GnomAD4 genome Cov.: 32

Bravo AF: 0.0000113

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:2 Benign:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

GeneDx

Jan 24, 2018

p.Arg895His (CGC>CAC): c.2684 G>A in exon 20 of the CACNA1C gene (NM_000719.6). The Arg895His variant in the CACNA1C gene has not been reported as a disease-causing mutation or as a benign polymorphism to our knowledge. Arg895His results in a conservative amino acid substitution of of one positively charged amino acid with another at a position that is conserved across species. In silico analysis predicts Arg895His is probably damaging to the protein structure/function. The Arg895His variant was not observed in approximately 6,000 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. Nevertheless, no mutations in nearby codons have been reported in association with LQTS, indicating this region of the protein may be tolerant of change. With the clinical and molecular information available at this time, we cannot definitively determine if Arg895His is a disease-causing mutation or a rare benign variant. The variant is found in LQT panel(s). -

Long QT syndrome Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jan 11, 2024

This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 895 of the CACNA1C protein (p.Arg895His). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with CACNA1C-related conditions. ClinVar contains an entry for this variant (Variation ID: 190656). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on CACNA1C protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Autism spectrum disorder Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Department of Genetics, Rouen University Hospital, Normandy Center for Genomic and Personalized Medicine

Aug 13, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.17	D
BayesDel_noAF	Uncertain	0.010
CADD	Pathogenic	32
DANN	Pathogenic	1.0
DEOGEN2	Benign	0.083	T;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;T;.;.;.;.;T;.
Eigen	Uncertain	0.61
Eigen_PC	Uncertain	0.59
FATHMM_MKL	Uncertain	0.93	D
M_CAP	Pathogenic	0.41	D
MetaRNN	Uncertain	0.67	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	Uncertain	2.5	.;M;.;M;M;M;M;M;M;M;M;M;M;M;M;M;.;M;M;M;.;.;.
PrimateAI	Uncertain	0.52	T
PROVEAN	Uncertain	-3.9	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
REVEL	Pathogenic	0.77
Sift	Benign	0.10	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
Sift4G	Benign	0.49	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
Polyphen		1.0, 0.87, 0.47, 0.99, 0.67, 1.0, 0.99, 0.99, 1.0, 0.99, 1.0, 1.0	.;D;P;P;D;P;D;D;D;P;D;D;D;D;D;D;.;D;D;.;D;.;D
Vest4		0.55
MutPred		0.61		.;Gain of catalytic residue at D899 (P = 0);Gain of catalytic residue at D899 (P = 0);Gain of catalytic residue at D899 (P = 0);Gain of catalytic residue at D899 (P = 0);Gain of catalytic residue at D899 (P = 0);Gain of catalytic residue at D899 (P = 0);Gain of catalytic residue at D899 (P = 0);Gain of catalytic residue at D899 (P = 0);Gain of catalytic residue at D899 (P = 0);Gain of catalytic residue at D899 (P = 0);Gain of catalytic residue at D899 (P = 0);Gain of catalytic residue at D899 (P = 0);Gain of catalytic residue at D899 (P = 0);Gain of catalytic residue at D899 (P = 0);Gain of catalytic residue at D899 (P = 0);Gain of catalytic residue at D899 (P = 0);Gain of catalytic residue at D899 (P = 0);Gain of catalytic residue at D899 (P = 0);Gain of catalytic residue at D899 (P = 0);Gain of catalytic residue at D899 (P = 0);Gain of catalytic residue at D899 (P = 0);Gain of catalytic residue at D899 (P = 0);
MVP		0.92
MPC		2.2
ClinPred		0.99	D
GERP RS		4.9
gMVP		0.63

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: rs786205755; hg19: chr12-2705060; COSMIC: COSV59705150;