chr12-2593261-G-C

Position:

• chr12-2593261-G-C

Variant summary

Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM1 PM2 PM5 PP2 PP3_Moderate PP5

The NM_000719.7(CACNA1C):​c.2579G>C​(p.Arg860Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R860G) has been classified as Likely pathogenic.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CACNA1C NM_000719.7 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1 U:3
• Conservation: PhyloP100: 8.08

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 Pathogenic. Variant got 10 ACMG points.

• PM1: In a region_of_interest Interaction with STAC2 (size 47) in uniprot entity CAC1C_HUMAN there are 7 pathogenic changes around while only 0 benign (100%) in NM_000719.7
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chrnull-null-null-null is described in UniProt as null.
• 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.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.862
• PP5: Variant 12-2593261-G-C is Pathogenic according to our data. Variant chr12-2593261-G-C is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 180284.We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=2, Likely_pathogenic=1}.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CACNA1C	NM_000719.7	c.2579G>C	p.Arg860Pro	missense_variant	19/47	ENST00000399655.6	NP_000710.5
CACNA1C	NM_001167623.2	c.2579G>C	p.Arg860Pro	missense_variant	19/47	ENST00000399603.6	NP_001161095.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CACNA1C	ENST00000399603.6	c.2579G>C	p.Arg860Pro	missense_variant	19/47	5	NM_001167623.2	ENSP00000382512.1
CACNA1C	ENST00000399655.6	c.2579G>C	p.Arg860Pro	missense_variant	19/47	1	NM_000719.7	ENSP00000382563.1
CACNA1C	ENST00000682544.1	c.2669G>C	p.Arg890Pro	missense_variant	19/50			ENSP00000507184.1
CACNA1C	ENST00000406454.8	c.2579G>C	p.Arg860Pro	missense_variant	19/48	5		ENSP00000385896.3
CACNA1C	ENST00000399634.6	c.2579G>C	p.Arg860Pro	missense_variant	19/47	5		ENSP00000382542.2
CACNA1C	ENST00000683824.1	c.2744G>C	p.Arg915Pro	missense_variant	20/48			ENSP00000507867.1
CACNA1C	ENST00000347598.9	c.2579G>C	p.Arg860Pro	missense_variant	19/49	1		ENSP00000266376.6
CACNA1C	ENST00000344100.7	c.2579G>C	p.Arg860Pro	missense_variant	19/47	1		ENSP00000341092.3
CACNA1C	ENST00000327702.12	c.2579G>C	p.Arg860Pro	missense_variant	19/48	1		ENSP00000329877.7
CACNA1C	ENST00000399617.6	c.2579G>C	p.Arg860Pro	missense_variant	19/48	5		ENSP00000382526.1
CACNA1C	ENST00000682462.1	c.2669G>C	p.Arg890Pro	missense_variant	19/47			ENSP00000507105.1
CACNA1C	ENST00000683781.1	c.2669G>C	p.Arg890Pro	missense_variant	19/47			ENSP00000507434.1
CACNA1C	ENST00000683840.1	c.2669G>C	p.Arg890Pro	missense_variant	19/47			ENSP00000507612.1
CACNA1C	ENST00000683956.1	c.2669G>C	p.Arg890Pro	missense_variant	19/47			ENSP00000506882.1
CACNA1C	ENST00000399638.5	c.2579G>C	p.Arg860Pro	missense_variant	19/48	1		ENSP00000382547.1
CACNA1C	ENST00000335762.10	c.2654G>C	p.Arg885Pro	missense_variant	20/48	5		ENSP00000336982.5
CACNA1C	ENST00000399606.5	c.2579G>C	p.Arg860Pro	missense_variant	19/48	1		ENSP00000382515.1
CACNA1C	ENST00000399621.5	c.2579G>C	p.Arg860Pro	missense_variant	19/47	1		ENSP00000382530.1
CACNA1C	ENST00000399637.5	c.2579G>C	p.Arg860Pro	missense_variant	19/47	1		ENSP00000382546.1
CACNA1C	ENST00000402845.7	c.2579G>C	p.Arg860Pro	missense_variant	19/47	1		ENSP00000385724.3
CACNA1C	ENST00000399629.5	c.2579G>C	p.Arg860Pro	missense_variant	19/47	1		ENSP00000382537.1
CACNA1C	ENST00000682336.1	c.2654G>C	p.Arg885Pro	missense_variant	20/47			ENSP00000507898.1
CACNA1C	ENST00000399591.5	c.2579G>C	p.Arg860Pro	missense_variant	19/46	1		ENSP00000382500.1
CACNA1C	ENST00000399595.5	c.2579G>C	p.Arg860Pro	missense_variant	19/46	1		ENSP00000382504.1
CACNA1C	ENST00000399649.5	c.2579G>C	p.Arg860Pro	missense_variant	19/46	1		ENSP00000382557.1
CACNA1C	ENST00000399597.5	c.2579G>C	p.Arg860Pro	missense_variant	19/47	1		ENSP00000382506.1
CACNA1C	ENST00000399601.5	c.2579G>C	p.Arg860Pro	missense_variant	19/47	1		ENSP00000382510.1
CACNA1C	ENST00000399641.6	c.2579G>C	p.Arg860Pro	missense_variant	19/47	1		ENSP00000382549.1
CACNA1C	ENST00000399644.5	c.2579G>C	p.Arg860Pro	missense_variant	19/47	1		ENSP00000382552.1
CACNA1C	ENST00000682835.1	c.2579G>C	p.Arg860Pro	missense_variant	19/47			ENSP00000507282.1
CACNA1C	ENST00000683482.1	c.2570G>C	p.Arg857Pro	missense_variant	19/47			ENSP00000507169.1
CACNA1C	ENST00000682686.1	c.2579G>C	p.Arg860Pro	missense_variant	19/46			ENSP00000507309.1
CACNA1C	ENST00000480911.6	n.*1186G>C		non_coding_transcript_exon_variant	17/27	5		ENSP00000437936.2
CACNA1C	ENST00000480911.6	n.*1186G>C		3_prime_UTR_variant	17/27	5		ENSP00000437936.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:1 Uncertain:3

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Long QT syndrome Uncertain:2

Uncertain significance, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Aug 24, 2019	This variant disrupts the p.Arg860 amino acid residue in CACNA1C. Other variant(s) that disrupt this residue have been observed in individuals with CACNA1C-related conditions (PMID: 25633834, 28600387), which suggests that this may be a clinically significant amino acid residue. 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. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). This variant has been observed in an individual with clinical features of long QT syndrome (Invitae). ClinVar contains an entry for this variant (Variation ID: 180284). This variant is not present in population databases (ExAC no frequency). This sequence change replaces arginine with proline at codon 860 of the CACNA1C protein (p.Arg860Pro). The arginine residue is highly conserved and there is a moderate physicochemical difference between arginine and proline. -
Uncertain significance, no assertion criteria provided	clinical testing	Blueprint Genetics	Aug 04, 2014	- -

Timothy syndrome Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Center For Human Genetics And Laboratory Diagnostics, Dr. Klein, Dr. Rost And Colleagues

May 18, 2018

- -

not provided Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Mar 07, 2016

Variant summary: CACNA1C c.2579G>C affects a conserved nucleotide, resulting in amino acid change from Arg to Pro. 3/4 in-silico tools predict this variant to be damaging (SNPs&GO not captured due to low reliability index). Another variant at this codon c.2579G>A (p.Arg860Gln) is classified as likely pathogenic in ClinVar and has been reported in the literature. However, the variant of interest has not been reported in affected individuals via publications and/or reputable databases; nor evaluated for functional impact by in vivo/vitro studies. Additionally, this variant was not found in 116972 control chromosomes. One clinical lab via ClinVar classified this variant as VUS, without evidence to independently evaluate. Because of the absence of clinical information and the lack of functional studies, the variant was classified as a variant of uncertain significance (VUS) until additional information becomes available. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.46	D
BayesDel_noAF	Pathogenic	0.43
CADD	Pathogenic	29
DANN	Uncertain	1.0
DEOGEN2	Benign	0.090	T;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;T;.;.;.;.;T;.
Eigen	Uncertain	0.57
Eigen_PC	Uncertain	0.50
FATHMM_MKL	Pathogenic	0.99	D
M_CAP	Pathogenic	0.73	D
MetaRNN	Pathogenic	0.86	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	2.8	.;M;.;M;M;M;M;M;M;M;M;M;M;M;M;M;.;M;M;M;.;.;.
PrimateAI	Pathogenic	0.81	D
PROVEAN	Pathogenic	-5.6	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	0.82
Sift	Uncertain	0.0010	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
Sift4G	Uncertain	0.054	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, 1.0, 0.11, 0.055, 0.21, 0.88, 1.0	.;D;D;B;B;B;D;D;D;P;D;D;D;D;D;D;.;D;D;.;D;.;D
Vest4		0.72
MutPred		0.33		.;Gain of catalytic residue at R860 (P = 0);Gain of catalytic residue at R860 (P = 0);Gain of catalytic residue at R860 (P = 0);Gain of catalytic residue at R860 (P = 0);Gain of catalytic residue at R860 (P = 0);Gain of catalytic residue at R860 (P = 0);Gain of catalytic residue at R860 (P = 0);Gain of catalytic residue at R860 (P = 0);Gain of catalytic residue at R860 (P = 0);Gain of catalytic residue at R860 (P = 0);Gain of catalytic residue at R860 (P = 0);Gain of catalytic residue at R860 (P = 0);Gain of catalytic residue at R860 (P = 0);Gain of catalytic residue at R860 (P = 0);Gain of catalytic residue at R860 (P = 0);Gain of catalytic residue at R860 (P = 0);Gain of catalytic residue at R860 (P = 0);Gain of catalytic residue at R860 (P = 0);Gain of catalytic residue at R860 (P = 0);Gain of catalytic residue at R860 (P = 0);Gain of catalytic residue at R860 (P = 0);Gain of catalytic residue at R860 (P = 0);
MVP		0.94
MPC		2.1
ClinPred		1.0	D
GERP RS		4.9
gMVP		0.92

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: rs730880056; hg19: chr12-2702427;