rs121908227

Positions:

• chr19-13261495-A-C

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.4205T>G​(p.Phe1402Cys) 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. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).

• Frequency: Genomes: not found (cov: 32)
• Consequence: CACNA1A NM_001127222.2 missense
• Clinical Significance: Pathogenic no assertion criteria provided P:1 O:1
• Conservation: PhyloP100: 9.29

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 III (size 283) in uniprot entity CAC1A_HUMAN there are 14 pathogenic changes around while only 1 benign (93%) in NM_001127222.2
• PM2: Very rare variant in population databases, with high coverage
• PP2: Missense variant in gene, where missense usually causes diseases (based on misZ statistic), CACNA1A. . Gene score misZ: 5.7845 (greater than the threshold 3.09). Trascript score misZ: 3.9354 (greater than threshold 3.09). The gene has 137 curated pathogenic missense variants (we use a threshold of 10). The gene has 132 curated benign missense variants. GenCC has associacion of the gene with 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, 0.921
• PP5: Variant 19-13261495-A-C is Pathogenic according to our data. Variant chr19-13261495-A-C is described in ClinVar as [Pathogenic]. Clinvar id is 8508.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.4205T>G	p.Phe1402Cys	missense_variant	26/47	ENST00000360228.11	NP_001120694.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CACNA1A	ENST00000360228.11	c.4205T>G	p.Phe1402Cys	missense_variant	26/47	1	NM_001127222.2	ENSP00000353362.5
CACNA1A	ENST00000638029.1	c.4217T>G	p.Phe1406Cys	missense_variant	26/48	5		ENSP00000489829.1
CACNA1A	ENST00000573710.7	c.4211T>G	p.Phe1404Cys	missense_variant	26/47	5		ENSP00000460092.3
CACNA1A	ENST00000635727.1	c.4208T>G	p.Phe1403Cys	missense_variant	26/47	5		ENSP00000490001.1
CACNA1A	ENST00000637769.1	c.4208T>G	p.Phe1403Cys	missense_variant	26/47	1		ENSP00000489778.1
CACNA1A	ENST00000636012.1	c.4208T>G	p.Phe1403Cys	missense_variant	26/46	5		ENSP00000490223.1
CACNA1A	ENST00000637736.1	c.4067T>G	p.Phe1356Cys	missense_variant	25/46	5		ENSP00000489861.1
CACNA1A	ENST00000636389.1	c.4208T>G	p.Phe1403Cys	missense_variant	26/47	5		ENSP00000489992.1
CACNA1A	ENST00000637432.1	c.4217T>G	p.Phe1406Cys	missense_variant	26/48	5		ENSP00000490617.1
CACNA1A	ENST00000636549.1	c.4208T>G	p.Phe1403Cys	missense_variant	26/48	5		ENSP00000490578.1
CACNA1A	ENST00000637927.1	c.4211T>G	p.Phe1404Cys	missense_variant	26/47	5		ENSP00000489715.1
CACNA1A	ENST00000635895.1	c.4208T>G	p.Phe1403Cys	missense_variant	26/47	5		ENSP00000490323.1
CACNA1A	ENST00000638009.2	c.4208T>G	p.Phe1403Cys	missense_variant	26/47	1		ENSP00000489913.1
CACNA1A	ENST00000637276.1	c.4208T>G	p.Phe1403Cys	missense_variant	26/46	5		ENSP00000489777.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

Alfa AF: 0.00209 Hom.: 0

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1 Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Episodic ataxia type 2 Pathogenic:1 Other:1

Pathogenic, no assertion criteria provided	literature only	OMIM	Nov 27, 2001	- -
not provided, no classification provided	literature only	UniProtKB/Swiss-Prot	-	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.58	D
BayesDel_noAF	Pathogenic	0.60
CADD	Pathogenic	32
DANN	Uncertain	0.98
DEOGEN2	Benign	0.38	.;.;T;.;.;.;.;.;.;T;.;.;.;T;.
Eigen	Pathogenic	0.80
Eigen_PC	Pathogenic	0.71
FATHMM_MKL	Uncertain	0.91	D
LIST_S2	Uncertain	0.97	D;D;D;D;D;D;D;D;.;D;D;D;D;D;D
M_CAP	Pathogenic	0.79	D
MetaRNN	Pathogenic	0.92	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	3.9	.;.;.;.;H;.;.;.;.;.;.;.;H;.;.
PrimateAI	Pathogenic	0.84	D
PROVEAN	Pathogenic	-7.9	.;D;.;.;.;.;.;.;.;.;.;.;.;.;.
REVEL	Pathogenic	0.94
Sift	Pathogenic	0.0	.;D;.;.;.;.;.;.;.;.;.;.;.;.;.
Sift4G	Pathogenic	0.0	D;D;.;.;.;.;.;.;.;.;.;.;.;.;.
Vest4		0.98
MutPred		0.61		.;.;Gain of methylation at K1402 (P = 0.0247);Gain of methylation at K1402 (P = 0.0247);Gain of methylation at K1402 (P = 0.0247);.;Gain of methylation at K1402 (P = 0.0247);.;.;Gain of methylation at K1402 (P = 0.0247);Gain of methylation at K1402 (P = 0.0247);.;Gain of methylation at K1402 (P = 0.0247);.;Gain of methylation at K1402 (P = 0.0247);
MVP		0.99
MPC		2.8
ClinPred		1.0	D
GERP RS		4.3
Varity_R		0.89
gMVP		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: rs121908227; hg19: chr19-13372309;