rs199473660

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 1P and 13B. PP2BP4_StrongBP6BS1BS2

The NM_000719.7(CACNA1C):​c.6040G>A​(p.Val2014Ile) variant causes a missense change. The variant allele was found at a frequency of 0.000249 in 1,610,992 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: 𝑓 0.00018 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00026 ( 0 hom. )

Consequence

CACNA1C
NM_000719.7 missense

Scores

1
2
13

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:8B:3O:1

Conservation

PhyloP100: 4.98
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 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.
BP4
Computational evidence support a benign effect (MetaRNN=0.046481907).
BP6
Variant 12-2688702-G-A is Benign according to our data. Variant chr12-2688702-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 67556.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=2, Uncertain_significance=6, not_provided=1, Benign=1}. Variant chr12-2688702-G-A is described in Lovd as [Likely_benign].
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.000184 (28/152282) while in subpopulation SAS AF= 0.00124 (6/4830). AF 95% confidence interval is 0.000541. There are 0 homozygotes in gnomad4. There are 16 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
High AC in GnomAd4 at 28 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CACNA1CNM_000719.7 linkuse as main transcriptc.6040G>A p.Val2014Ile missense_variant 46/47 ENST00000399655.6 NP_000710.5 Q13936-12
CACNA1CNM_001167623.2 linkuse as main transcriptc.6040G>A p.Val2014Ile missense_variant 46/47 ENST00000399603.6 NP_001161095.1 Q13936-37

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CACNA1CENST00000399603.6 linkuse as main transcriptc.6040G>A p.Val2014Ile missense_variant 46/475 NM_001167623.2 ENSP00000382512.1 Q13936-37
CACNA1CENST00000399655.6 linkuse as main transcriptc.6040G>A p.Val2014Ile missense_variant 46/471 NM_000719.7 ENSP00000382563.1 Q13936-12
CACNA1CENST00000682544.1 linkuse as main transcriptc.6379G>A p.Val2127Ile missense_variant 49/50 ENSP00000507184.1 A0A804HIR0
CACNA1CENST00000406454.8 linkuse as main transcriptc.6253G>A p.Val2085Ile missense_variant 47/485 ENSP00000385896.3 F5GY28
CACNA1CENST00000399634.6 linkuse as main transcriptc.6220G>A p.Val2074Ile missense_variant 46/475 ENSP00000382542.2 E9PDI6
CACNA1CENST00000683824.1 linkuse as main transcriptc.6205G>A p.Val2069Ile missense_variant 47/48 ENSP00000507867.1 A0A804HKC4
CACNA1CENST00000347598.9 linkuse as main transcriptc.6184G>A p.Val2062Ile missense_variant 48/491 ENSP00000266376.6 Q13936-11
CACNA1CENST00000344100.7 linkuse as main transcriptc.6163G>A p.Val2055Ile missense_variant 46/471 ENSP00000341092.3 Q13936-14
CACNA1CENST00000327702.12 linkuse as main transcriptc.6145G>A p.Val2049Ile missense_variant 47/481 ENSP00000329877.7 A0A0A0MR67
CACNA1CENST00000399617.6 linkuse as main transcriptc.6145G>A p.Val2049Ile missense_variant 47/485 ENSP00000382526.1 A0A0A0MSA1
CACNA1CENST00000682462.1 linkuse as main transcriptc.6130G>A p.Val2044Ile missense_variant 46/47 ENSP00000507105.1 A0A804HIJ8
CACNA1CENST00000683781.1 linkuse as main transcriptc.6130G>A p.Val2044Ile missense_variant 46/47 ENSP00000507434.1 A0A804HJB6
CACNA1CENST00000683840.1 linkuse as main transcriptc.6130G>A p.Val2044Ile missense_variant 46/47 ENSP00000507612.1 A0A804HJR1
CACNA1CENST00000683956.1 linkuse as main transcriptc.6130G>A p.Val2044Ile missense_variant 46/47 ENSP00000506882.1 A0A804HI37
CACNA1CENST00000399638.5 linkuse as main transcriptc.6124G>A p.Val2042Ile missense_variant 47/481 ENSP00000382547.1 Q13936-31
CACNA1CENST00000335762.10 linkuse as main transcriptc.6115G>A p.Val2039Ile missense_variant 47/485 ENSP00000336982.5 F5H522
CACNA1CENST00000399606.5 linkuse as main transcriptc.6100G>A p.Val2034Ile missense_variant 47/481 ENSP00000382515.1 Q13936-30
CACNA1CENST00000399621.5 linkuse as main transcriptc.6097G>A p.Val2033Ile missense_variant 46/471 ENSP00000382530.1 Q13936-24
CACNA1CENST00000399637.5 linkuse as main transcriptc.6097G>A p.Val2033Ile missense_variant 46/471 ENSP00000382546.1 Q13936-27
CACNA1CENST00000402845.7 linkuse as main transcriptc.6097G>A p.Val2033Ile missense_variant 46/471 ENSP00000385724.3 Q13936-13
CACNA1CENST00000399629.5 linkuse as main transcriptc.6091G>A p.Val2031Ile missense_variant 46/471 ENSP00000382537.1 Q13936-32
CACNA1CENST00000682336.1 linkuse as main transcriptc.6082G>A p.Val2028Ile missense_variant 46/47 ENSP00000507898.1 A0A804HKE9
CACNA1CENST00000399591.5 linkuse as main transcriptc.6064G>A p.Val2022Ile missense_variant 45/461 ENSP00000382500.1 Q13936-29
CACNA1CENST00000399595.5 linkuse as main transcriptc.6064G>A p.Val2022Ile missense_variant 45/461 ENSP00000382504.1 Q13936-25
CACNA1CENST00000399649.5 linkuse as main transcriptc.6058G>A p.Val2020Ile missense_variant 45/461 ENSP00000382557.1 Q13936-15
CACNA1CENST00000399597.5 linkuse as main transcriptc.6040G>A p.Val2014Ile missense_variant 46/471 ENSP00000382506.1 Q13936-22
CACNA1CENST00000399601.5 linkuse as main transcriptc.6040G>A p.Val2014Ile missense_variant 46/471 ENSP00000382510.1 Q13936-20
CACNA1CENST00000399641.6 linkuse as main transcriptc.6040G>A p.Val2014Ile missense_variant 46/471 ENSP00000382549.1 Q13936-23
CACNA1CENST00000399644.5 linkuse as main transcriptc.6040G>A p.Val2014Ile missense_variant 46/471 ENSP00000382552.1 Q13936-21
CACNA1CENST00000682835.1 linkuse as main transcriptc.6040G>A p.Val2014Ile missense_variant 46/47 ENSP00000507282.1 A0A804HIZ0
CACNA1CENST00000683482.1 linkuse as main transcriptc.6031G>A p.Val2011Ile missense_variant 46/47 ENSP00000507169.1 Q13936-35
CACNA1CENST00000682686.1 linkuse as main transcriptc.6007G>A p.Val2003Ile missense_variant 45/46 ENSP00000507309.1 Q13936-19

Frequencies

GnomAD3 genomes
AF:
0.000184
AC:
28
AN:
152164
Hom.:
0
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.000121
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.0000654
Gnomad ASJ
AF:
0.000576
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00124
Gnomad FIN
AF:
0.000377
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000147
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000345
AC:
83
AN:
240516
Hom.:
0
AF XY:
0.000388
AC XY:
51
AN XY:
131376
show subpopulations
Gnomad AFR exome
AF:
0.000414
Gnomad AMR exome
AF:
0.0000586
Gnomad ASJ exome
AF:
0.000511
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.000825
Gnomad FIN exome
AF:
0.000885
Gnomad NFE exome
AF:
0.000231
Gnomad OTH exome
AF:
0.000339
GnomAD4 exome
AF:
0.000256
AC:
373
AN:
1458710
Hom.:
0
Cov.:
33
AF XY:
0.000274
AC XY:
199
AN XY:
725598
show subpopulations
Gnomad4 AFR exome
AF:
0.0000897
Gnomad4 AMR exome
AF:
0.0000674
Gnomad4 ASJ exome
AF:
0.000768
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.000825
Gnomad4 FIN exome
AF:
0.000749
Gnomad4 NFE exome
AF:
0.000203
Gnomad4 OTH exome
AF:
0.000199
GnomAD4 genome
AF:
0.000184
AC:
28
AN:
152282
Hom.:
0
Cov.:
33
AF XY:
0.000215
AC XY:
16
AN XY:
74458
show subpopulations
Gnomad4 AFR
AF:
0.000120
Gnomad4 AMR
AF:
0.0000653
Gnomad4 ASJ
AF:
0.000576
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00124
Gnomad4 FIN
AF:
0.000377
Gnomad4 NFE
AF:
0.000147
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000387
Hom.:
0
Bravo
AF:
0.000193
TwinsUK
AF:
0.000270
AC:
1
ALSPAC
AF:
0.000259
AC:
1
ESP6500AA
AF:
0.000261
AC:
1
ESP6500EA
AF:
0.000488
AC:
4
ExAC
AF:
0.000357
AC:
43
EpiCase
AF:
0.000218
EpiControl
AF:
0.000238

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:8Benign:3Other:1
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

not provided Uncertain:3Benign:1
Uncertain significance, criteria provided, single submitterclinical testingRevvity Omics, RevvityAug 11, 2022- -
Likely benign, criteria provided, single submitterclinical testingCeGaT Center for Human Genetics TuebingenNov 01, 2024CACNA1C: BP4 -
Uncertain significance, criteria provided, single submitterclinical testingGeneDxNov 09, 2016p.Val2014Ile (GTC>ATC): c.6040 G>A in exon 46 in the CACNA1C gene (NM_000719.6). The V2014I variant was not observed with any significant frequency in approximately 6000 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The V2014I variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved across species. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. A recent publication classifies V2014I as a variant of unknown significance (Dorschner et al., 2013). The variant is found in LQT panel(s). -
Uncertain significance, criteria provided, single submitterclinical testingEurofins Ntd Llc (ga)Mar 11, 2015- -
not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingLaboratory for Molecular Medicine, Mass General Brigham Personalized MedicineApr 25, 2016Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: 4 papers in HGMD, 3 reference presence in control databases; ExAC: 0.1% (19/13788) South Asian chromosomes -
CACNA1C-related disorder Uncertain:1
Uncertain significance, no assertion criteria providedclinical testingPreventionGenetics, part of Exact SciencesMar 27, 2024The CACNA1C c.6040G>A variant is predicted to result in the amino acid substitution p.Val2014Ile. This variant was reported in individuals with Brugada syndrome (Table1, Burashnikov et al. 2010. PubMed ID: 20817017; Risgaard et al. 2013. PubMed ID: 23414114). This variant is mainly classified as likely benign/uncertain by multiple publications (Table S1, Dorschner et al. 2013. PubMed ID: 24055113; Amendola et al. 2015. PubMed ID: 25637381; Marschall et al. 2019. PubMed ID: 31737537; Maltese et al. 2019. PubMed ID: 31539150 ) and likely pathogenic by one publication (Campuzano et al. 2019. PubMed ID: 30821013). This variant is reported in 0.082% of alleles in individuals of South Asian descent in gnomAD. In ClinVar, this variant has conflicting interpretations of benign, likely benign, and uncertain (https://www.ncbi.nlm.nih.gov/clinvar/variation/67556/?new_evidence=true). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -
Brugada syndrome (shorter-than-normal QT interval) Uncertain:1
Uncertain significance, no assertion criteria providedresearchCSER _CC_NCGL, University of WashingtonJun 01, 2014- -
Brugada syndrome 3 Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingCenter For Human Genetics And Laboratory Diagnostics, Dr. Klein, Dr. Rost And ColleaguesMar 17, 2018- -
Timothy syndrome Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingMendelicsMay 28, 2019- -
Long QT syndrome Benign:1
Likely benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 29, 2024- -
Cardiovascular phenotype Benign:1
Benign, criteria provided, single submitterclinical testingAmbry GeneticsJan 10, 2022This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. -
Brugada syndrome Other:1
not provided, no classification providedliterature onlyCardiovascular Biomedical Research Unit, Royal Brompton & Harefield NHS Foundation Trust-This variant has been reported as associated with Brugada syndrome in the following publications (PMID:20817017). This is a literature report, and does not necessarily reflect the clinical interpretation of the Imperial College / Royal Brompton Cardiovascular Genetics laboratory. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
-0.41
T
BayesDel_noAF
Benign
-0.44
CADD
Uncertain
23
DANN
Uncertain
0.99
DEOGEN2
Benign
0.011
T;.;.;.;.;.;.;.;.;.;.;.;.;.;.;T;.;.;.;.;T;.;T
Eigen
Benign
0.11
Eigen_PC
Benign
0.18
FATHMM_MKL
Pathogenic
0.98
D
M_CAP
Benign
0.058
D
MetaRNN
Benign
0.046
T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
-0.85
T
PrimateAI
Uncertain
0.52
T
PROVEAN
Benign
-0.68
N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;N;.
REVEL
Benign
0.12
Sift
Benign
0.051
T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;D;T;D;D;D;.
Sift4G
Benign
0.17
T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
Polyphen
0.53, 0.43, 0.44, 0.18, 0.59, 0.64, 0.76, 0.93, 0.81
.;P;B;B;B;P;P;P;B;P;P;P;P;P;P;.;P;P;.;.;.;P;.
Vest4
0.49
MVP
0.53
MPC
0.17
ClinPred
0.029
T
GERP RS
5.2
gMVP
0.47

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs199473660; hg19: chr12-2797868; COSMIC: COSV59772541; COSMIC: COSV59772541; API