12-2605088-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PM2PP2PP3_Moderate

The NM_000719.7(CACNA1C):​c.2968G>C​(p.Ala990Pro) 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 Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Consequence

CACNA1C
NM_000719.7 missense

Scores

11
5
1

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 10.0
Variant links:
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]
CACNA1C-AS3 (HGNC:40117): (CACNA1C antisense RNA 3)

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 5 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.
PP3
MetaRNN computational evidence supports a deleterious effect, 0.88

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CACNA1CNM_000719.7 linkc.2968G>C p.Ala990Pro missense_variant 23/47 ENST00000399655.6 NP_000710.5 Q13936-12
CACNA1CNM_001167623.2 linkc.2968G>C p.Ala990Pro missense_variant 23/47 ENST00000399603.6 NP_001161095.1 Q13936-37

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CACNA1CENST00000399603.6 linkc.2968G>C p.Ala990Pro missense_variant 23/475 NM_001167623.2 ENSP00000382512.1 Q13936-37
CACNA1CENST00000399655.6 linkc.2968G>C p.Ala990Pro missense_variant 23/471 NM_000719.7 ENSP00000382563.1 Q13936-12
CACNA1CENST00000682544.1 linkc.3118G>C p.Ala1040Pro missense_variant 24/50 ENSP00000507184.1 A0A804HIR0
CACNA1CENST00000406454.8 linkc.2968G>C p.Ala990Pro missense_variant 23/485 ENSP00000385896.3 F5GY28
CACNA1CENST00000399634.6 linkc.2968G>C p.Ala990Pro missense_variant 23/475 ENSP00000382542.2 E9PDI6
CACNA1CENST00000683824.1 linkc.3133G>C p.Ala1045Pro missense_variant 24/48 ENSP00000507867.1 A0A804HKC4
CACNA1CENST00000347598.9 linkc.3028G>C p.Ala1010Pro missense_variant 24/491 ENSP00000266376.6 Q13936-11
CACNA1CENST00000344100.7 linkc.2968G>C p.Ala990Pro missense_variant 23/471 ENSP00000341092.3 Q13936-14
CACNA1CENST00000327702.12 linkc.2968G>C p.Ala990Pro missense_variant 23/481 ENSP00000329877.7 A0A0A0MR67
CACNA1CENST00000399617.6 linkc.2968G>C p.Ala990Pro missense_variant 23/485 ENSP00000382526.1 A0A0A0MSA1
CACNA1CENST00000682462.1 linkc.3058G>C p.Ala1020Pro missense_variant 23/47 ENSP00000507105.1 A0A804HIJ8
CACNA1CENST00000683781.1 linkc.3058G>C p.Ala1020Pro missense_variant 23/47 ENSP00000507434.1 A0A804HJB6
CACNA1CENST00000683840.1 linkc.3058G>C p.Ala1020Pro missense_variant 23/47 ENSP00000507612.1 A0A804HJR1
CACNA1CENST00000683956.1 linkc.3058G>C p.Ala1020Pro missense_variant 23/47 ENSP00000506882.1 A0A804HI37
CACNA1CENST00000399638.5 linkc.2968G>C p.Ala990Pro missense_variant 23/481 ENSP00000382547.1 Q13936-31
CACNA1CENST00000335762.10 linkc.3043G>C p.Ala1015Pro missense_variant 24/485 ENSP00000336982.5 F5H522
CACNA1CENST00000399606.5 linkc.3028G>C p.Ala1010Pro missense_variant 24/481 ENSP00000382515.1 Q13936-30
CACNA1CENST00000399621.5 linkc.2968G>C p.Ala990Pro missense_variant 23/471 ENSP00000382530.1 Q13936-24
CACNA1CENST00000399637.5 linkc.2968G>C p.Ala990Pro missense_variant 23/471 ENSP00000382546.1 Q13936-27
CACNA1CENST00000402845.7 linkc.2968G>C p.Ala990Pro missense_variant 23/471 ENSP00000385724.3 Q13936-13
CACNA1CENST00000399629.5 linkc.2968G>C p.Ala990Pro missense_variant 23/471 ENSP00000382537.1 Q13936-32
CACNA1CENST00000682336.1 linkc.3043G>C p.Ala1015Pro missense_variant 24/47 ENSP00000507898.1 A0A804HKE9
CACNA1CENST00000399591.5 linkc.2968G>C p.Ala990Pro missense_variant 23/461 ENSP00000382500.1 Q13936-29
CACNA1CENST00000399595.5 linkc.2968G>C p.Ala990Pro missense_variant 23/461 ENSP00000382504.1 Q13936-25
CACNA1CENST00000399649.5 linkc.2968G>C p.Ala990Pro missense_variant 23/461 ENSP00000382557.1 Q13936-15
CACNA1CENST00000399597.5 linkc.2968G>C p.Ala990Pro missense_variant 23/471 ENSP00000382506.1 Q13936-22
CACNA1CENST00000399601.5 linkc.2968G>C p.Ala990Pro missense_variant 23/471 ENSP00000382510.1 Q13936-20
CACNA1CENST00000399641.6 linkc.2968G>C p.Ala990Pro missense_variant 23/471 ENSP00000382549.1 Q13936-23
CACNA1CENST00000399644.5 linkc.2968G>C p.Ala990Pro missense_variant 23/471 ENSP00000382552.1 Q13936-21
CACNA1CENST00000682835.1 linkc.2968G>C p.Ala990Pro missense_variant 23/47 ENSP00000507282.1 A0A804HIZ0
CACNA1CENST00000683482.1 linkc.2959G>C p.Ala987Pro missense_variant 23/47 ENSP00000507169.1 Q13936-35
CACNA1CENST00000682686.1 linkc.2968G>C p.Ala990Pro missense_variant 23/46 ENSP00000507309.1 Q13936-19
CACNA1CENST00000480911.6 linkn.*1575G>C non_coding_transcript_exon_variant 21/275 ENSP00000437936.2 F5H638
CACNA1CENST00000480911.6 linkn.*1575G>C 3_prime_UTR_variant 21/275 ENSP00000437936.2 F5H638

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
30
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

Cardiovascular phenotype Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsJul 24, 2023The p.A990P variant (also known as c.2968G>C), located in coding exon 23 of the CACNA1C gene, results from a G to C substitution at nucleotide position 2968. The alanine at codon 990 is replaced by proline, an amino acid with highly similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
0.50
D
BayesDel_noAF
Pathogenic
0.48
CADD
Pathogenic
29
DANN
Uncertain
1.0
DEOGEN2
Uncertain
0.66
D;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;T;.;.;.;.;T;.
Eigen
Pathogenic
0.80
Eigen_PC
Pathogenic
0.76
FATHMM_MKL
Pathogenic
0.99
D
M_CAP
Pathogenic
0.69
D
MetaRNN
Pathogenic
0.88
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
2.3
.;.;.;.;.;.;.;.;.;.;.;M;M;.;.;.;.;.;.;.;.;.;.
PrimateAI
Pathogenic
0.89
D
PROVEAN
Pathogenic
-4.8
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
0.90
Sift
Uncertain
0.013
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
0.026
D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
Polyphen
1.0, 1.0, 0.71, 1.0, 0.82
.;D;D;P;D;D;D;D;D;P;D;D;D;D;D;D;.;D;D;.;.;.;D
Vest4
0.81
MutPred
0.58
.;.;.;.;.;.;.;.;.;.;.;Gain of catalytic residue at Q1007 (P = 0.0112);Gain of catalytic residue at Q1007 (P = 0.0112);.;.;.;.;.;.;.;.;.;.;
MVP
0.96
MPC
1.6
ClinPred
0.99
D
GERP RS
4.5
gMVP
0.99

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr12-2714254; API