rs1555774867

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM1PM2PP2PP3

The NM_001127222.2(CACNA1A):​c.643G>A​(p.Val215Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,370 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).

Frequency

Genomes: not found (cov: 31)
Exomes 𝑓: 0.0000014 ( 0 hom. )

Consequence

CACNA1A
NM_001127222.2 missense

Scores

7
10
2

Clinical Significance

Uncertain significance criteria provided, multiple submitters, no conflicts U:2

Conservation

PhyloP100: 7.81
Variant links:
Genes affected
CACNA1A (HGNC:1388): (calcium voltage-gated channel subunit alpha1 A) Voltage-dependent calcium channels mediate the entry of calcium ions into excitable cells, and are also involved in a variety of calcium-dependent processes, including muscle contraction, hormone or neurotransmitter release, and gene expression. Calcium channels are multisubunit complexes composed of alpha-1, beta, alpha-2/delta, and gamma subunits. The channel activity is directed by the pore-forming alpha-1 subunit, whereas, the others act as auxiliary subunits regulating this activity. The distinctive properties of the calcium channel types are related primarily to the expression of a variety of alpha-1 isoforms, alpha-1A, B, C, D, E, and S. This gene encodes the alpha-1A subunit, which is predominantly expressed in neuronal tissue. Mutations in this gene are associated with 2 neurologic disorders, familial hemiplegic migraine and episodic ataxia 2. This gene also exhibits polymorphic variation due to (CAG)n-repeats. Multiple transcript variants encoding different isoforms have been found for this gene. In one set of transcript variants, the (CAG)n-repeats occur in the 3' UTR, and are not associated with any disease. But in another set of variants, an insertion extends the coding region to include the (CAG)n-repeats which encode a polyglutamine tract. Expansion of the (CAG)n-repeats from the normal 4-18 to 21-33 in the coding region is associated with spinocerebellar ataxia 6. [provided by RefSeq, Jul 2016]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_pathogenic. Variant got 6 ACMG points.

PM1
In a repeat I (size 278) in uniprot entity CAC1A_HUMAN there are 11 pathogenic changes around while only 1 benign (92%) in NM_001127222.2
PM2
Very rare variant in population databases, with high coverage;
PP2
Missense variant in gene, where missense usually causes diseases (based on misZ statistic), CACNA1A. . Gene score misZ 5.7845 (greater than the threshold 3.09). Trascript score misZ 3.9354 (greater than threshold 3.09). GenCC has associacion of gene with benign paroxysmal torticollis of infancy, developmental and epileptic encephalopathy, 42, undetermined early-onset epileptic encephalopathy, episodic ataxia type 2, familial or sporadic hemiplegic migraine, spinocerebellar ataxia type 6, Lennox-Gastaut syndrome, migraine, familial hemiplegic, 1.
PP3
MetaRNN computational evidence supports a deleterious effect, 0.768

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
CACNA1ANM_001127222.2 linkuse as main transcriptc.643G>A p.Val215Ile missense_variant 5/47 ENST00000360228.11 NP_001120694.1 O00555-8

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
CACNA1AENST00000360228.11 linkuse as main transcriptc.643G>A p.Val215Ile missense_variant 5/471 NM_001127222.2 ENSP00000353362.5 O00555-8
CACNA1AENST00000638029.1 linkuse as main transcriptc.643G>A p.Val215Ile missense_variant 5/485 ENSP00000489829.1 A0A087WW63
CACNA1AENST00000573710.7 linkuse as main transcriptc.643G>A p.Val215Ile missense_variant 5/475 ENSP00000460092.3 A0A1C7CYY9
CACNA1AENST00000635727.1 linkuse as main transcriptc.643G>A p.Val215Ile missense_variant 5/475 ENSP00000490001.1 A0A1B0GU81
CACNA1AENST00000637769.1 linkuse as main transcriptc.643G>A p.Val215Ile missense_variant 5/471 ENSP00000489778.1 A0A1B0GTN7
CACNA1AENST00000636012.1 linkuse as main transcriptc.643G>A p.Val215Ile missense_variant 5/465 ENSP00000490223.1 A0A1B0GUS3
CACNA1AENST00000637736.1 linkuse as main transcriptc.502G>A p.Val168Ile missense_variant 4/465 ENSP00000489861.1 A0A1B0GTW2
CACNA1AENST00000636389.1 linkuse as main transcriptc.643G>A p.Val215Ile missense_variant 5/475 ENSP00000489992.1 A0A1B0GU74
CACNA1AENST00000637432.1 linkuse as main transcriptc.643G>A p.Val215Ile missense_variant 5/485 ENSP00000490617.1 O00555-2
CACNA1AENST00000636549.1 linkuse as main transcriptc.643G>A p.Val215Ile missense_variant 5/485 ENSP00000490578.1 B5TYJ1
CACNA1AENST00000637927.1 linkuse as main transcriptc.643G>A p.Val215Ile missense_variant 5/475 ENSP00000489715.1 A0A1B0GTI4
CACNA1AENST00000635895.1 linkuse as main transcriptc.643G>A p.Val215Ile missense_variant 5/475 ENSP00000490323.1 A0A384DVW2
CACNA1AENST00000638009.2 linkuse as main transcriptc.643G>A p.Val215Ile missense_variant 5/471 ENSP00000489913.1 O00555-3
CACNA1AENST00000637276.1 linkuse as main transcriptc.643G>A p.Val215Ile missense_variant 5/465 ENSP00000489777.1 O00555-5

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
AF:
0.00000137
AC:
2
AN:
1461370
Hom.:
0
Cov.:
31
AF XY:
0.00000138
AC XY:
1
AN XY:
726968
show subpopulations
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:
0.00000180
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
31

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAthena DiagnosticsFeb 21, 2017- -
Episodic ataxia type 2;C4310716:Developmental and epileptic encephalopathy, 42 Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpMay 08, 2017In summary, this variant is a novel missense change with uncertain impact on protein function. It has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive, but these predictions have not been confirmed by published functional studies. This variant is not present in population databases (ExAC no frequency) and has not been reported in the literature in individuals with a CACNA1A-related disease. This sequence change replaces valine with isoleucine at codon 215 of the CACNA1A protein (p.Val215Ile). The valine residue is highly conserved and there is a small physicochemical difference between valine and isoleucine. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.44
BayesDel_addAF
Pathogenic
0.21
D
BayesDel_noAF
Uncertain
0.070
CADD
Pathogenic
29
DANN
Uncertain
1.0
DEOGEN2
Uncertain
0.70
.;D;T;.;.;.;.;.;.;T;.;.;.;T;.
Eigen
Uncertain
0.36
Eigen_PC
Uncertain
0.40
FATHMM_MKL
Uncertain
0.97
D
LIST_S2
Pathogenic
0.99
D;D;D;D;D;D;D;D;.;D;D;D;D;D;D
M_CAP
Pathogenic
0.38
D
MetaRNN
Pathogenic
0.77
D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM
Pathogenic
0.97
D
MutationAssessor
Uncertain
2.4
.;M;.;.;M;.;.;M;.;.;.;.;M;.;.
PrimateAI
Pathogenic
0.85
D
PROVEAN
Benign
-0.84
.;N;.;.;.;.;.;.;.;.;.;.;.;.;.
REVEL
Pathogenic
0.70
Sift
Uncertain
0.0070
.;D;.;.;.;.;.;.;.;.;.;.;.;.;.
Sift4G
Uncertain
0.014
D;D;.;.;.;.;.;.;.;.;.;D;.;.;.
Polyphen
0.95
.;P;.;.;.;.;.;.;.;.;.;.;.;.;.
Vest4
0.37
MutPred
0.60
Gain of MoRF binding (P = 0.2078);Gain of MoRF binding (P = 0.2078);Gain of MoRF binding (P = 0.2078);Gain of MoRF binding (P = 0.2078);Gain of MoRF binding (P = 0.2078);.;Gain of MoRF binding (P = 0.2078);Gain of MoRF binding (P = 0.2078);Gain of MoRF binding (P = 0.2078);Gain of MoRF binding (P = 0.2078);Gain of MoRF binding (P = 0.2078);Gain of MoRF binding (P = 0.2078);Gain of MoRF binding (P = 0.2078);Gain of MoRF binding (P = 0.2078);Gain of MoRF binding (P = 0.2078);
MVP
0.89
MPC
1.6
ClinPred
0.96
D
GERP RS
4.5
Varity_R
0.54
gMVP
0.86

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.010
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: rs1555774867; hg19: chr19-13476272; API