rs1555758842

Variant names:

• chr19-13308121-G-A
• rs1555758842
• NM_001127222.2:c.1912C>T

Variant summary

Our verdict is Pathogenic. The variant received 13 ACMG points: 13P and 0B. PVS1 PM2 PP3 PP5_Moderate

The NM_001127222.2(CACNA1A):​c.1912C>T​(p.Gln638*) variant causes a stop gained, splice region change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CACNA1A NM_001127222.2 stop_gained, splice_region
• Scores: Splicing: ADA: 0.9695
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 3.96

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

Our verdict: Pathogenic. The variant received 13 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
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF. No scorers claiming Uncertain. Scorers claiming Benign: max_spliceai.
• PP5: Variant 19-13308121-G-A is Pathogenic according to our data. Variant chr19-13308121-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 520652.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr19-13308121-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNA1A	NM_001127222.2	c.1912C>T	p.Gln638*	stop_gained, splice_region_variant	Exon 14 of 47	ENST00000360228.11	NP_001120694.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CACNA1A	ENST00000360228.11	c.1912C>T	p.Gln638*	stop_gained, splice_region_variant	Exon 14 of 47	1	NM_001127222.2	ENSP00000353362.5
CACNA1A	ENST00000638029.1	c.1915C>T	p.Gln639*	stop_gained, splice_region_variant	Exon 14 of 48	5		ENSP00000489829.1
CACNA1A	ENST00000573710.7	c.1918C>T	p.Gln640*	stop_gained, splice_region_variant	Exon 14 of 47	5		ENSP00000460092.3
CACNA1A	ENST00000635727.1	c.1915C>T	p.Gln639*	stop_gained, splice_region_variant	Exon 14 of 47	5		ENSP00000490001.1
CACNA1A	ENST00000637769.1	c.1915C>T	p.Gln639*	stop_gained, splice_region_variant	Exon 14 of 47	1		ENSP00000489778.1
CACNA1A	ENST00000636012.1	c.1915C>T	p.Gln639*	stop_gained, splice_region_variant	Exon 14 of 46	5		ENSP00000490223.1
CACNA1A	ENST00000637736.1	c.1774C>T	p.Gln592*	stop_gained, splice_region_variant	Exon 13 of 46	5		ENSP00000489861.1
CACNA1A	ENST00000636389.1	c.1915C>T	p.Gln639*	stop_gained, splice_region_variant	Exon 14 of 47	5		ENSP00000489992.1
CACNA1A	ENST00000637432.1	c.1915C>T	p.Gln639*	stop_gained, splice_region_variant	Exon 14 of 48	5		ENSP00000490617.1
CACNA1A	ENST00000636549.1	c.1915C>T	p.Gln639*	stop_gained, splice_region_variant	Exon 14 of 48	5		ENSP00000490578.1
CACNA1A	ENST00000637927.1	c.1918C>T	p.Gln640*	stop_gained, splice_region_variant	Exon 14 of 47	5		ENSP00000489715.1
CACNA1A	ENST00000635895.1	c.1915C>T	p.Gln639*	stop_gained, splice_region_variant	Exon 14 of 47	5		ENSP00000490323.1
CACNA1A	ENST00000638009.2	c.1915C>T	p.Gln639*	stop_gained, splice_region_variant	Exon 14 of 47	1		ENSP00000489913.1
CACNA1A	ENST00000637276.1	c.1915C>T	p.Gln639*	stop_gained, splice_region_variant	Exon 14 of 46	5		ENSP00000489777.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Inborn genetic diseases Pathogenic:1

Mar 31, 2015

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.63	D
BayesDel_noAF	Pathogenic	0.66
CADD	Pathogenic	43
DANN	Uncertain	1.0
Eigen	Pathogenic	0.89
Eigen_PC	Pathogenic	0.72
FATHMM_MKL	Uncertain	0.94	D
Vest4		0.91
GERP RS		5.1
Mutation Taster		=0/200	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	0.97
dbscSNV1_RF	Pathogenic	0.87
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: rs1555758842; hg19: chr19-13418935;