19-13253021-A-C

Variant names:

• chr19-13253021-A-C
• rs781413708
• NM_001127222.2:c.4836T>G

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.4836T>G​(p.Cys1612Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,184 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★). Synonymous variant affecting the same amino acid position (i.e. C1612C) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000021 (0 hom.)
• Consequence: CACNA1A NM_001127222.2 missense
• Clinical Significance: Uncertain significance criteria provided, multiple submitters, no conflicts U:3
• Conservation: PhyloP100: 0.276
• Publications: 0 publications found

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

ACMG classification

Our verdict: Likely_pathogenic. The variant received 6 ACMG points.

• PM1: In a repeat IV (size 263) in uniprot entity CAC1A_HUMAN there are 39 pathogenic changes around while only 10 benign (80%) in NM_001127222.2
• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.882

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNA1A	NM_001127222.2	c.4836T>G	p.Cys1612Trp	missense_variant	Exon 30 of 47	ENST00000360228.11	NP_001120694.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CACNA1A	ENST00000360228.11	c.4836T>G	p.Cys1612Trp	missense_variant	Exon 30 of 47	1	NM_001127222.2	ENSP00000353362.5
CACNA1A	ENST00000638029.1	c.4848T>G	p.Cys1616Trp	missense_variant	Exon 30 of 48	5		ENSP00000489829.1
CACNA1A	ENST00000573710.7	c.4842T>G	p.Cys1614Trp	missense_variant	Exon 30 of 47	5		ENSP00000460092.3
CACNA1A	ENST00000635727.1	c.4839T>G	p.Cys1613Trp	missense_variant	Exon 30 of 47	5		ENSP00000490001.1
CACNA1A	ENST00000637769.1	c.4839T>G	p.Cys1613Trp	missense_variant	Exon 30 of 47	1		ENSP00000489778.1
CACNA1A	ENST00000636012.1	c.4839T>G	p.Cys1613Trp	missense_variant	Exon 30 of 46	5		ENSP00000490223.1
CACNA1A	ENST00000637736.1	c.4698T>G	p.Cys1566Trp	missense_variant	Exon 29 of 46	5		ENSP00000489861.1
CACNA1A	ENST00000636389.1	c.4839T>G	p.Cys1613Trp	missense_variant	Exon 30 of 47	5		ENSP00000489992.1
CACNA1A	ENST00000637432.1	c.4848T>G	p.Cys1616Trp	missense_variant	Exon 30 of 48	5		ENSP00000490617.1
CACNA1A	ENST00000636549.1	c.4839T>G	p.Cys1613Trp	missense_variant	Exon 30 of 48	5		ENSP00000490578.1
CACNA1A	ENST00000637927.1	c.4842T>G	p.Cys1614Trp	missense_variant	Exon 30 of 47	5		ENSP00000489715.1
CACNA1A	ENST00000635895.1	c.4839T>G	p.Cys1613Trp	missense_variant	Exon 30 of 47	5		ENSP00000490323.1
CACNA1A	ENST00000638009.2	c.4839T>G	p.Cys1613Trp	missense_variant	Exon 30 of 47	1		ENSP00000489913.1
CACNA1A	ENST00000637276.1	c.4839T>G	p.Cys1613Trp	missense_variant	Exon 30 of 46	5		ENSP00000489777.1
CACNA1A	ENST00000636768.2	n.4839T>G		non_coding_transcript_exon_variant	Exon 30 of 45	5		ENSP00000490190.2
CACNA1A	ENST00000713789.1	n.4836T>G		non_coding_transcript_exon_variant	Exon 30 of 47			ENSP00000519091.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD2 exomes AF: 0.0000120 AC: 3 AN: 249158 AF XY: 0.00000740

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000266

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000205 AC: 3 AN: 1461184 Hom.: 0 Cov.: 29 AF XY: 0.00000138 AC XY: 1 AN XY: 726926

African (AFR) AF: 0.00 AC: 0 AN: 33464

American (AMR) AF: 0.00 AC: 0 AN: 44720

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26128

East Asian (EAS) AF: 0.00 AC: 0 AN: 39696

South Asian (SAS) AF: 0.00 AC: 0 AN: 86244

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53376

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5768

European-Non Finnish (NFE) AF: 0.00000270 AC: 3 AN: 1111438

Other (OTH) AF: 0.00 AC: 0 AN: 60350

GnomAD4 genome Cov.: 32

Alfa AF: 0.0000434 Hom.: 0

Bravo AF: 0.0000113

ExAC AF: 0.0000165 AC: 2

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

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

Mar 11, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces cysteine, which is neutral and slightly polar, with tryptophan, which is neutral and slightly polar, at codon 1613 of the CACNA1A protein (p.Cys1613Trp). This variant is present in population databases (rs781413708, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with CACNA1A-related conditions. ClinVar contains an entry for this variant (Variation ID: 393096). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt CACNA1A protein function with a negative predictive value of 95%. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -

Inborn genetic diseases Uncertain:1

Aug 02, 2022

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.4839T>G (p.C1613W) alteration is located in exon 30 (coding exon 30) of the CACNA1A gene. This alteration results from a T to G substitution at nucleotide position 4839, causing the cysteine (C) at amino acid position 1613 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

not provided Uncertain:1

Nov 10, 2024

GeneDx

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.99
BayesDel_addAF	Pathogenic	0.28	D
BayesDel_noAF	Pathogenic	0.23
CADD	Benign	22
DANN	Benign	0.97
DEOGEN2	Benign	0.35	.;.;T;.;.;.;.;.;.;.;T;.;.;.;T;.;.
Eigen	Benign	-0.20
Eigen_PC	Benign	-0.51
FATHMM_MKL	Benign	0.087	N
LIST_S2	Uncertain	0.96	D;D;D;D;D;D;D;D;D;.;D;D;D;D;D;D;D
M_CAP	Pathogenic	0.85	D
MetaRNN	Pathogenic	0.88	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	4.3	.;.;.;.;H;.;.;.;.;.;.;.;.;H;.;.;.
PhyloP100		0.28
PrimateAI	Pathogenic	0.81	D
PROVEAN	Pathogenic	-9.9	.;D;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.
REVEL	Uncertain	0.64
Sift	Pathogenic	0.0	.;D;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.
Sift4G	Pathogenic	0.0010	D;D;.;.;.;D;.;.;.;.;.;.;.;.;.;.;.
Vest4		0.71
MutPred		0.71		.;.;Gain of catalytic residue at L1611 (P = 0.0029);Gain of catalytic residue at L1611 (P = 0.0029);Gain of catalytic residue at L1611 (P = 0.0029);.;.;Gain of catalytic residue at L1611 (P = 0.0029);.;.;Gain of catalytic residue at L1611 (P = 0.0029);Gain of catalytic residue at L1611 (P = 0.0029);.;Gain of catalytic residue at L1611 (P = 0.0029);.;Gain of catalytic residue at L1611 (P = 0.0029);.;
MVP		0.99
MPC		2.8
ClinPred		1.0	D
GERP RS		-1.6
PromoterAI		-0.034	Neutral
Varity_R		0.95
gMVP		0.99
Mutation Taster		=80/20	polymorphism

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

Other links and lift over

dbSNP: rs781413708; hg19: chr19-13363835;