19-13275925-C-T

Variant names:

• chr19-13275925-C-T
• NM_001127222.2:c.3914G>A

Variant summary

Our verdict is Likely pathogenic. The variant received 6 ACMG points: 6P and 0B. PM1 PM2 PP3_Moderate

The NM_001127222.2(CACNA1A):​c.3914G>A​(p.Gly1305Asp) 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G1305V) has been classified as Uncertain significance.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CACNA1A NM_001127222.2 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 7.79

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: Likely_pathogenic. The variant received 6 ACMG points.

• PM1: In a repeat III (size 283) in uniprot entity CAC1A_HUMAN there are 75 pathogenic changes around while only 10 benign (88%) in NM_001127222.2
• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.897

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNA1A	NM_001127222.2	c.3914G>A	p.Gly1305Asp	missense_variant	Exon 24 of 47	ENST00000360228.11	NP_001120694.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CACNA1A	ENST00000360228.11	c.3914G>A	p.Gly1305Asp	missense_variant	Exon 24 of 47	1	NM_001127222.2	ENSP00000353362.5
CACNA1A	ENST00000638029.1	c.3926G>A	p.Gly1309Asp	missense_variant	Exon 24 of 48	5		ENSP00000489829.1
CACNA1A	ENST00000573710.7	c.3920G>A	p.Gly1307Asp	missense_variant	Exon 24 of 47	5		ENSP00000460092.3
CACNA1A	ENST00000635727.1	c.3917G>A	p.Gly1306Asp	missense_variant	Exon 24 of 47	5		ENSP00000490001.1
CACNA1A	ENST00000637769.1	c.3917G>A	p.Gly1306Asp	missense_variant	Exon 24 of 47	1		ENSP00000489778.1
CACNA1A	ENST00000636012.1	c.3917G>A	p.Gly1306Asp	missense_variant	Exon 24 of 46	5		ENSP00000490223.1
CACNA1A	ENST00000637736.1	c.3776G>A	p.Gly1259Asp	missense_variant	Exon 23 of 46	5		ENSP00000489861.1
CACNA1A	ENST00000636389.1	c.3917G>A	p.Gly1306Asp	missense_variant	Exon 24 of 47	5		ENSP00000489992.1
CACNA1A	ENST00000637432.1	c.3926G>A	p.Gly1309Asp	missense_variant	Exon 24 of 48	5		ENSP00000490617.1
CACNA1A	ENST00000636549.1	c.3917G>A	p.Gly1306Asp	missense_variant	Exon 24 of 48	5		ENSP00000490578.1
CACNA1A	ENST00000637927.1	c.3920G>A	p.Gly1307Asp	missense_variant	Exon 24 of 47	5		ENSP00000489715.1
CACNA1A	ENST00000635895.1	c.3917G>A	p.Gly1306Asp	missense_variant	Exon 24 of 47	5		ENSP00000490323.1
CACNA1A	ENST00000638009.2	c.3917G>A	p.Gly1306Asp	missense_variant	Exon 24 of 47	1		ENSP00000489913.1
CACNA1A	ENST00000637276.1	c.3917G>A	p.Gly1306Asp	missense_variant	Exon 24 of 46	5		ENSP00000489777.1
CACNA1A	ENST00000636768.2	n.3917G>A		non_coding_transcript_exon_variant	Exon 24 of 45	5		ENSP00000490190.2
CACNA1A	ENST00000713789.1	n.3914G>A		non_coding_transcript_exon_variant	Exon 24 of 47			ENSP00000519091.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.98
BayesDel_addAF	Pathogenic	0.37	D
BayesDel_noAF	Pathogenic	0.29
CADD	Pathogenic	29
DANN	Uncertain	1.0
DEOGEN2	Benign	0.24	.;.;T;.;.;.;.;.;.;T;.;.;.;T;.
Eigen	Uncertain	0.68
Eigen_PC	Uncertain	0.64
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Pathogenic	0.97	D;D;D;D;D;D;D;D;.;D;D;D;D;D;D
M_CAP	Pathogenic	0.60	D
MetaRNN	Pathogenic	0.90	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Uncertain	2.5	.;.;.;.;M;.;.;.;.;.;.;.;M;.;.
PhyloP100		7.8
PrimateAI	Pathogenic	0.87	D
PROVEAN	Pathogenic	-6.5	.;D;.;.;.;.;.;.;.;.;.;.;.;.;.
REVEL	Pathogenic	0.86
Sift	Uncertain	0.0020	.;D;.;.;.;.;.;.;.;.;.;.;.;.;.
Sift4G	Uncertain	0.0020	D;D;.;.;.;.;.;.;.;.;.;.;.;.;.
Vest4		0.72
MutPred		0.68		.;.;Gain of relative solvent accessibility (P = 0.09);Gain of relative solvent accessibility (P = 0.09);Gain of relative solvent accessibility (P = 0.09);.;Gain of relative solvent accessibility (P = 0.09);.;.;Gain of relative solvent accessibility (P = 0.09);Gain of relative solvent accessibility (P = 0.09);.;Gain of relative solvent accessibility (P = 0.09);.;Gain of relative solvent accessibility (P = 0.09);
MVP		0.89
MPC		2.8
ClinPred		0.99	D
GERP RS		4.5
Varity_R		0.83
gMVP		0.98
Mutation Taster		=13/87	disease causing

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.050		Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr19-13386739;