rs587776694

Positions:

• chr19-13298819-G-GC

Variant summary

Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PVS1 PM2 PP5

The NM_001127222.2(CACNA1A):​c.2813dupG​(p.Ser939fs) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000705 in 1,418,418 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (no stars). Variant results in nonsense mediated mRNA decay.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 7.1e-7 (0 hom.)
• Consequence: CACNA1A NM_001127222.2 frameshift
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 0.199

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 Pathogenic. Variant got 11 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 19-13298819-G-GC is Pathogenic according to our data. Variant chr19-13298819-G-GC is described in ClinVar as [Pathogenic]. Clinvar id is 8501.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CACNA1A	NM_001127222.2	c.2813dupG	p.Ser939fs	frameshift_variant	19/47	ENST00000360228.11	NP_001120694.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CACNA1A	ENST00000360228.11	c.2813dupG	p.Ser939fs	frameshift_variant	19/47	1	NM_001127222.2	ENSP00000353362.5
CACNA1A	ENST00000638029.1	c.2825dupG	p.Ser943fs	frameshift_variant	19/48	5		ENSP00000489829.1
CACNA1A	ENST00000573710.7	c.2819dupG	p.Ser941fs	frameshift_variant	19/47	5		ENSP00000460092.3
CACNA1A	ENST00000635727.1	c.2816dupG	p.Ser940fs	frameshift_variant	19/47	5		ENSP00000490001.1
CACNA1A	ENST00000637769.1	c.2816dupG	p.Ser940fs	frameshift_variant	19/47	1		ENSP00000489778.1
CACNA1A	ENST00000636012.1	c.2816dupG	p.Ser940fs	frameshift_variant	19/46	5		ENSP00000490223.1
CACNA1A	ENST00000637736.1	c.2675dupG	p.Ser893fs	frameshift_variant	18/46	5		ENSP00000489861.1
CACNA1A	ENST00000636389.1	c.2816dupG	p.Ser940fs	frameshift_variant	19/47	5		ENSP00000489992.1
CACNA1A	ENST00000637432.1	c.2825dupG	p.Ser943fs	frameshift_variant	19/48	5		ENSP00000490617.1
CACNA1A	ENST00000636549.1	c.2816dupG	p.Ser940fs	frameshift_variant	19/48	5		ENSP00000490578.1
CACNA1A	ENST00000637927.1	c.2819dupG	p.Ser941fs	frameshift_variant	19/47	5		ENSP00000489715.1
CACNA1A	ENST00000635895.1	c.2816dupG	p.Ser940fs	frameshift_variant	19/47	5		ENSP00000490323.1
CACNA1A	ENST00000638009.2	c.2816dupG	p.Ser940fs	frameshift_variant	19/47	1		ENSP00000489913.1
CACNA1A	ENST00000637276.1	c.2816dupG	p.Ser940fs	frameshift_variant	19/46	5		ENSP00000489777.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 7.05e-7 AC: 1 AN: 1418418 Hom.: 0 Cov.: 32 AF XY: 0.00000142 AC XY: 1 AN XY: 704450

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: 0.00

Gnomad4 OTH exome AF: 0.0000170

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Episodic ataxia type 2 Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Apr 01, 2001

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs587776694; hg19: chr19-13409633;