19-13452889-C-T

Variant names:

• chr19-13452889-C-T
• rs1057521920
• NM_001127222.2:c.526G>A

Variant summary

Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM1 PM2 PP2 PP3_Moderate PP5

The NM_001127222.2(CACNA1A):​c.526G>A​(p.Val176Met) 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).

• Frequency: Genomes: not found (cov: 32)
• Consequence: CACNA1A NM_001127222.2 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:2 U:2
• Conservation: PhyloP100: 7.76

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]

ACMG classification

Verdict is Likely_pathogenic. Variant got 8 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 the CACNA1A gene, where missense mutations are typically associated with disease (based on misZ statistic). The gene has 137 curated pathogenic missense variants (we use a threshold of 10). The gene has 132 curated benign missense variants. Gene score misZ: 5.7845 (above the threshold of 3.09). Trascript score misZ: 3.9354 (above the threshold of 3.09). GenCC associations: The gene is linked to 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, 0.907
• PP5: Variant 19-13452889-C-T is Pathogenic according to our data. Variant chr19-13452889-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 426878.We mark this variant Likely_pathogenic, oryginal submissions are: {Likely_pathogenic=1, Uncertain_significance=2, Pathogenic=1}.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNA1A	NM_001127222.2	c.526G>A	p.Val176Met	missense_variant	Exon 3 of 47	ENST00000360228.11	NP_001120694.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CACNA1A	ENST00000360228.11	c.526G>A	p.Val176Met	missense_variant	Exon 3 of 47	1	NM_001127222.2	ENSP00000353362.5
CACNA1A	ENST00000638029.1	c.526G>A	p.Val176Met	missense_variant	Exon 3 of 48	5		ENSP00000489829.1
CACNA1A	ENST00000573710.7	c.526G>A	p.Val176Met	missense_variant	Exon 3 of 47	5		ENSP00000460092.3
CACNA1A	ENST00000635727.1	c.526G>A	p.Val176Met	missense_variant	Exon 3 of 47	5		ENSP00000490001.1
CACNA1A	ENST00000637769.1	c.526G>A	p.Val176Met	missense_variant	Exon 3 of 47	1		ENSP00000489778.1
CACNA1A	ENST00000636012.1	c.526G>A	p.Val176Met	missense_variant	Exon 3 of 46	5		ENSP00000490223.1
CACNA1A	ENST00000637736.1	c.385G>A	p.Val129Met	missense_variant	Exon 2 of 46	5		ENSP00000489861.1
CACNA1A	ENST00000636389.1	c.526G>A	p.Val176Met	missense_variant	Exon 3 of 47	5		ENSP00000489992.1
CACNA1A	ENST00000637432.1	c.526G>A	p.Val176Met	missense_variant	Exon 3 of 48	5		ENSP00000490617.1
CACNA1A	ENST00000636549.1	c.526G>A	p.Val176Met	missense_variant	Exon 3 of 48	5		ENSP00000490578.1
CACNA1A	ENST00000637927.1	c.526G>A	p.Val176Met	missense_variant	Exon 3 of 47	5		ENSP00000489715.1
CACNA1A	ENST00000635895.1	c.526G>A	p.Val176Met	missense_variant	Exon 3 of 47	5		ENSP00000490323.1
CACNA1A	ENST00000638009.2	c.526G>A	p.Val176Met	missense_variant	Exon 3 of 47	1		ENSP00000489913.1
CACNA1A	ENST00000637276.1	c.526G>A	p.Val176Met	missense_variant	Exon 3 of 46	5		ENSP00000489777.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:2 Uncertain:2

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Pathogenic:1 Uncertain:1

Oct 01, 2019

CeGaT Center for Human Genetics Tuebingen

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Oct 23, 2017

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The V176M variant in the CACNA1A gene has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The V176M variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The V176M variant has been identified as a de novo variant in two individuals previously tested at GeneDx. This substitution occurs at a position that is conserved across species, and in silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. The V176M variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. The V176M variant is considered a pathogenic variant. -

CACNA1A-related disorder Pathogenic:1

Jun 05, 2023

Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

PS2, PS4_Supporting, PM2, PP2, PP3 -

Episodic ataxia type 2;C4310716:Developmental and epileptic encephalopathy, 42 Uncertain:1

Jul 06, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces valine, which is neutral and non-polar, with methionine, which is neutral and non-polar, at codon 176 of the CACNA1A protein (p.Val176Met). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with developmental and epileptic encephalopathy (PMID: 29455050, 33057194). ClinVar contains an entry for this variant (Variation ID: 426878). 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) performed at Invitae indicates that this missense variant is expected to disrupt CACNA1A protein function with a positive predictive value of 95%. 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. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.96
BayesDel_addAF	Pathogenic	0.53	D
BayesDel_noAF	Pathogenic	0.52
CADD	Pathogenic	30
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.92	.;D;T;.;.;.;.;.;.;T;.;.;.;T;.;.
Eigen	Pathogenic	0.99
Eigen_PC	Pathogenic	0.94
FATHMM_MKL	Pathogenic	1.0	D
LIST_S2	Pathogenic	0.99	D;D;D;D;D;D;D;D;.;D;D;D;D;D;D;.
M_CAP	Pathogenic	0.65	D
MetaRNN	Pathogenic	0.91	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	3.0	.;M;.;.;M;.;.;M;.;.;.;.;M;.;.;.
PrimateAI	Pathogenic	0.86	D
PROVEAN	Benign	-2.3	.;N;.;.;.;.;.;.;.;.;.;.;.;.;.;.
REVEL	Pathogenic	0.92
Sift	Pathogenic	0.0	.;D;.;.;.;.;.;.;.;.;.;.;.;.;.;.
Sift4G	Pathogenic	0.0010	D;D;.;.;.;.;.;.;.;.;.;D;.;.;.;D
Polyphen		1.0	.;D;.;.;.;.;.;.;.;.;.;.;.;.;.;.
Vest4		0.76
MutPred		0.68		Loss of catalytic residue at V176 (P = 0.1363);Loss of catalytic residue at V176 (P = 0.1363);Loss of catalytic residue at V176 (P = 0.1363);Loss of catalytic residue at V176 (P = 0.1363);Loss of catalytic residue at V176 (P = 0.1363);.;Loss of catalytic residue at V176 (P = 0.1363);Loss of catalytic residue at V176 (P = 0.1363);Loss of catalytic residue at V176 (P = 0.1363);Loss of catalytic residue at V176 (P = 0.1363);Loss of catalytic residue at V176 (P = 0.1363);Loss of catalytic residue at V176 (P = 0.1363);Loss of catalytic residue at V176 (P = 0.1363);Loss of catalytic residue at V176 (P = 0.1363);Loss of catalytic residue at V176 (P = 0.1363);.;
MVP		0.98
MPC		2.0
ClinPred		1.0	D
GERP RS		5.8
Varity_R		0.86
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: rs1057521920; hg19: chr19-13563703;