rs121909323

Variant names:

Variant summary

Our verdict is Pathogenic. The variant received 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong

The NM_001127222.2(CACNA1A):c.3829C>T(p.Arg1277*) 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 Pathogenic (★★). Variant results in nonsense mediated mRNA decay.

Frequency

Genomes: not found (cov: 31)

Consequence

CACNA1A
NM_001127222.2 stop_gained

Scores

Clinical Significance

Pathogenic criteria provided, multiple submitters, no conflicts P:5

Conservation

PhyloP100: 3.21

Publications

6 publications found

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]

CACNA1A Gene-Disease associations (from GenCC):

episodic ataxia type 2
Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Ambry Genetics, Genomics England PanelApp, Labcorp Genetics (formerly Invitae)
undetermined early-onset epileptic encephalopathy
Inheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: Orphanet, Illumina
developmental and epileptic encephalopathy, 42
Inheritance: AD Classification: STRONG, MODERATE Submitted by: G2P, Ambry Genetics, Labcorp Genetics (formerly Invitae)
migraine, familial hemiplegic, 1
Inheritance: AD Classification: STRONG Submitted by: Ambry Genetics, Genomics England PanelApp, Labcorp Genetics (formerly Invitae)
spinocerebellar ataxia type 6
Inheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Ambry Genetics, Genomics England PanelApp, Labcorp Genetics (formerly Invitae), Orphanet
benign paroxysmal torticollis of infancy
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
familial or sporadic hemiplegic migraine
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
Lennox-Gastaut syndrome
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

CACNA1A links:

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ACMG classification

Classification was made for transcript

Our verdict: Pathogenic. The variant received 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 19-13277122-G-A is Pathogenic according to our data. Variant chr19-13277122-G-A is described in ClinVar as Pathogenic. ClinVar VariationId is 8506.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNA1A	NM_001127222.2 link	c.3829C>T	p.Arg1277*	stop_gained	Exon 23 of 47	ENST00000360228.11	NP_001120694.1
CACNA1A	NM_001127221.2 link	c.3832C>T	p.Arg1278*	stop_gained	Exon 23 of 47	ENST00000638009.2	NP_001120693.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein
CACNA1A	ENST00000360228.11 link	c.3829C>T	p.Arg1277*	stop_gained	Exon 23 of 47	1	NM_001127222.2	ENSP00000353362.5
CACNA1A	ENST00000638009.2 link	c.3832C>T	p.Arg1278*	stop_gained	Exon 23 of 47	1	NM_001127221.2	ENSP00000489913.1
CACNA1A	ENST00000638029.1 link	c.3841C>T	p.Arg1281*	stop_gained	Exon 23 of 48	5		ENSP00000489829.1
CACNA1A	ENST00000573710.7 link	c.3835C>T	p.Arg1279*	stop_gained	Exon 23 of 47	5		ENSP00000460092.3
CACNA1A	ENST00000635727.1 link	c.3832C>T	p.Arg1278*	stop_gained	Exon 23 of 47	5		ENSP00000490001.1
CACNA1A	ENST00000637769.1 link	c.3832C>T	p.Arg1278*	stop_gained	Exon 23 of 47	1		ENSP00000489778.1
CACNA1A	ENST00000636012.1 link	c.3832C>T	p.Arg1278*	stop_gained	Exon 23 of 46	5		ENSP00000490223.1
CACNA1A	ENST00000637736.1 link	c.3691C>T	p.Arg1231*	stop_gained	Exon 22 of 46	5		ENSP00000489861.1
CACNA1A	ENST00000636389.1 link	c.3832C>T	p.Arg1278*	stop_gained	Exon 23 of 47	5		ENSP00000489992.1
CACNA1A	ENST00000637432.1 link	c.3841C>T	p.Arg1281*	stop_gained	Exon 23 of 48	5		ENSP00000490617.1
CACNA1A	ENST00000636549.1 link	c.3832C>T	p.Arg1278*	stop_gained	Exon 23 of 48	5		ENSP00000490578.1
CACNA1A	ENST00000637927.1 link	c.3835C>T	p.Arg1279*	stop_gained	Exon 23 of 47	5		ENSP00000489715.1
CACNA1A	ENST00000635895.1 link	c.3832C>T	p.Arg1278*	stop_gained	Exon 23 of 47	5		ENSP00000490323.1
CACNA1A	ENST00000637276.1 link	c.3832C>T	p.Arg1278*	stop_gained	Exon 23 of 46	5		ENSP00000489777.1
CACNA1A	ENST00000636768.2 link	n.3832C>T		non_coding_transcript_exon_variant	Exon 23 of 45	5		ENSP00000490190.2
CACNA1A	ENST00000713789.1 link	n.3829C>T		non_coding_transcript_exon_variant	Exon 23 of 47			ENSP00000519091.1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Cov.:

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:5

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Episodic ataxia type 2

Pathogenic:2

Nov 25, 2014

E. Rossignol Lab, CHU Ste-Justine, Universite de Montreal

Significance:Pathogenic

Review Status:no assertion criteria provided

Collection Method:clinical testing

- -

Nov 27, 2001

OMIM

Significance:Pathogenic

Review Status:no assertion criteria provided

Collection Method:literature only

- -

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

Pathogenic:1

Feb 23, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Pathogenic

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This sequence change creates a premature translational stop signal (p.Arg1278*) 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). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with CACNA1A-related conditions (PMID: 9600739, 25735478, 25784583). In at least one individual the variant was observed to be de novo. This variant is also known as c.4110C>T (p.Arg1279*). ClinVar contains an entry for this variant (Variation ID: 8506). For these reasons, this variant has been classified as Pathogenic. -

not provided

Pathogenic:1

Dec 22, 2023

GeneDx

Significance:Pathogenic

Review Status:criteria provided, single submitter

Collection Method:clinical testing

Published functional studies demonstrate a damaging effect as variant leads to markedly decreased current densities compared to wild type (PMID: 11723274); 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: 25525159, 11742003, 16306128, 28167673, 11723274, 32899500, 9600739, 25735478, 27667184, 25784583) -

CACNA1A-related complex neurodevelopmental disorder

Pathogenic:1

Oct 08, 2024

Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

Significance:Pathogenic

Review Status:criteria provided, single submitter

Collection Method:clinical testing

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. Type 2 episodic ataxia (MIM#108500) is mostly associated with loss of function, while familial hemiplegic migraine 1, with or without progressive cerebellar ataxia (MIM#141500) is associated with gain of function. Developmental and epileptic encephalopathy 42 (MIM#617106) is associated with both mechanisms, and spinocerebellar ataxia 6 (MIM#183086) is associated with CAG repeat expansion (OMIM, PMID: 25735478, 28566750, 31468518, 32116539). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0112 - The condition associated with this gene has incomplete penetrance. Asymptomatic family members have been reported to carry the same variant as affected family members (PMID: 10408533, 30142438). (I) 0115 - Variants in this gene are known to have variable expressivity. Intrafamilial variability has been reported for episodic ataxia, intellectual disability and/or epilepsy (PMID: 30142438, 32910250). (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 - Many other NMD-predicted variants comparable to the one identified in this case have very strong previous evidence for pathogenicity (DECIPHER). (SP) 0802 - This variant has moderate previous evidence of pathogenicity in unrelated individuals. This variant has been classified as pathogenic in ClinVar and has been observed in two unrelated families with CACNA1A-related symptoms. (PMID: 25735478, 25784583). (SP) 1206 - This variant has been shown to be paternally inherited (by trio analysis). (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Pathogenic

0.63

BayesDel_noAF

Pathogenic

0.58

CADD

Pathogenic

(source)

DANN

Uncertain

1.0

Eigen

Pathogenic

0.70

Eigen_PC

Uncertain

0.53

FATHMM_MKL

Uncertain

0.86

PhyloP100

3.2

Vest4

0.96

GERP RS

3.6

Mutation Taster

=0/200

disease causing (ClinVar)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

Splicevardb

2.0

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over