chr19-13255217-G-A

Position:

• chr19-13255217-G-A

Variant summary

Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1 PM2 PP5_Very_Strong

The NM_001127222.2(CACNA1A):​c.4633C>T​(p.Arg1545*) variant causes a stop gained change involving the alteration of a non-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 Likely pathogenic (★★). Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 30)
• Consequence: CACNA1A NM_001127222.2 stop_gained
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:9
• Conservation: PhyloP100: 3.31

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 18 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 19-13255217-G-A is Pathogenic according to our data. Variant chr19-13255217-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 8507.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr19-13255217-G-A is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CACNA1A	NM_001127222.2	c.4633C>T	p.Arg1545*	stop_gained	29/47	ENST00000360228.11	NP_001120694.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CACNA1A	ENST00000360228.11	c.4633C>T	p.Arg1545*	stop_gained	29/47	1	NM_001127222.2	ENSP00000353362.5
CACNA1A	ENST00000638029.1	c.4645C>T	p.Arg1549*	stop_gained	29/48	5		ENSP00000489829.1
CACNA1A	ENST00000573710.7	c.4639C>T	p.Arg1547*	stop_gained	29/47	5		ENSP00000460092.3
CACNA1A	ENST00000635727.1	c.4636C>T	p.Arg1546*	stop_gained	29/47	5		ENSP00000490001.1
CACNA1A	ENST00000637769.1	c.4636C>T	p.Arg1546*	stop_gained	29/47	1		ENSP00000489778.1
CACNA1A	ENST00000636012.1	c.4636C>T	p.Arg1546*	stop_gained	29/46	5		ENSP00000490223.1
CACNA1A	ENST00000637736.1	c.4495C>T	p.Arg1499*	stop_gained	28/46	5		ENSP00000489861.1
CACNA1A	ENST00000636389.1	c.4636C>T	p.Arg1546*	stop_gained	29/47	5		ENSP00000489992.1
CACNA1A	ENST00000637432.1	c.4645C>T	p.Arg1549*	stop_gained	29/48	5		ENSP00000490617.1
CACNA1A	ENST00000636549.1	c.4636C>T	p.Arg1546*	stop_gained	29/48	5		ENSP00000490578.1
CACNA1A	ENST00000637927.1	c.4639C>T	p.Arg1547*	stop_gained	29/47	5		ENSP00000489715.1
CACNA1A	ENST00000635895.1	c.4636C>T	p.Arg1546*	stop_gained	29/47	5		ENSP00000490323.1
CACNA1A	ENST00000638009.2	c.4636C>T	p.Arg1546*	stop_gained	29/47	1		ENSP00000489913.1
CACNA1A	ENST00000637276.1	c.4636C>T	p.Arg1546*	stop_gained	29/46	5		ENSP00000489777.1

Frequencies

GnomAD3 genomes Cov.: 30

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 30

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:9

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Episodic ataxia type 2 Pathogenic:4

Likely pathogenic, criteria provided, single submitter	curation	SIB Swiss Institute of Bioinformatics	Oct 15, 2018	This variant is interpreted as Likely Pathogenic, for Episodic ataxia 2, autosomal dominant. The following ACMG Tag(s) were applied: PM2 => Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium. PVS1-Strong => PVS1 downgraded in strength to Strong. PP1-Moderate => PP1 upgraded in strength to Moderate (https://www.ncbi.nlm.nih.gov/pubmed/10408533). -
Pathogenic, no assertion criteria provided	literature only	OMIM	Jul 13, 1999	- -
Pathogenic, criteria provided, single submitter	clinical testing	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	Feb 02, 2022	Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0103 - Loss of function and gain of function are known mechanisms of disease in this gene and are associated with CACNA1A-related disease. Episodic ataxia, type 2 (MIM#108500) is caused by variants with a loss of function mechanism (PMID: 28566750). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0112 - The condition associated with this gene has incomplete penetrance. Reduced penetrance has been reported for patients with episodic ataxia type 2 (OMIM). (I) 0115 - Variants in this gene are known to have variable expressivity. Two families with episodic ataxia, intellectual disability and/or epilepsy have been reported with intrafamilial variability (PMID: 32910250, PMID: 30142438). (I) 0201 - Variant is predicted to cause nonsense-mediated decay (NMD) and loss of protein (premature termination codon is located at least 54 nucleotides upstream of the final exon-exon junction). (SP) 0251 - This variant is heterozygous. (I) 0301 - Variant is absent from gnomAD (both v2 and v3). (SP) 0701 - Other variants predicted to result in NMD comparable to the one identified in this case have very strong previous evidence for pathogenicity (DECIPHER, ClinVar). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. It has been previously reported in patients with episodic ataxia type 2 (ClinVar, PMID: 10408533, PMID: 29883219). (SP) 1102 - Strong phenotype match for this individual. (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -
Pathogenic, criteria provided, single submitter	research	HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology	Oct 25, 2019	ACMG codes: PVS1, PS3, PM2, PP5 -

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Dec 09, 2022	Described as R1549X and R1547X using alternate nomenclature, published functional studies demonstrate markedly decreased current densities compared to wild type (Jen et al., 2001; Jeng et al., 2006); Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 10408533, 29062094, 29482223, 16306128, 25525159, 29883219, 11723274) -
Pathogenic, criteria provided, single submitter	clinical testing	Athena Diagnostics	Apr 08, 2022	This variant segregates with episodic ataxia in at least one family. This variant was not reported in large, multi-ethnic, general populations (http://gnomad.broadinstitute.org). In some published literature, this variant is referred to as p.R1549X. Assessment of experimental evidence suggests this variant results in abnormal protein function. This variant diminished calcium channel activity (PMID: 11723274, 16306128). -

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

Pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jun 07, 2023

For these reasons, this variant has been classified as Pathogenic. Experimental studies have shown that this premature translational stop signal affects CACNA1A function (PMID: 11723274). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. ClinVar contains an entry for this variant (Variation ID: 8507). This variant is also known as p.Arg1549*. This premature translational stop signal has been observed in individual(s) with CACNA1A-related conditions (PMID: 29062094, 29883219, 31302675). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Arg1546*) in the CACNA1A gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CACNA1A are known to be pathogenic (PMID: 10371528, 19486177, 25735478, 27250579). -

Inborn genetic diseases Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Oct 11, 2016

- -

Spinocerebellar ataxia type 6;C1720416:Episodic ataxia type 2;C1832884:Migraine, familial hemiplegic, 1;C4310716:Developmental and epileptic encephalopathy, 42 Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Sep 05, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.63	D
BayesDel_noAF	Pathogenic	0.46
CADD	Pathogenic	36
DANN	Uncertain	1.0
Eigen	Uncertain	0.39
Eigen_PC	Benign	0.15
FATHMM_MKL	Uncertain	0.94	D
Vest4		0.96
GERP RS		1.0

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: rs121909324; hg19: chr19-13366031;