19-13298647-GGCCCTCGCCCTC-G

Position:

• chr19-13298647-GGCCCTCGCCCTC-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM4 BS2

The NM_001127222.2(CACNA1A):​c.2974_2985delGAGGGCGAGGGC​(p.Glu992_Gly995del) variant causes a conservative inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000513 in 1,365,414 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★★).

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000051 (0 hom.)
• Consequence: CACNA1A NM_001127222.2 conservative_inframe_deletion
• Clinical Significance: Uncertain significance criteria provided, multiple submitters, no conflicts U:2
• Conservation: PhyloP100: 1.85

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_benign. Variant got -2 ACMG points.

• PM4: Nonframeshift variant in NON repetitive region in NM_001127222.2.
• BS2: High AC in GnomAdExome4 at 7 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CACNA1A	NM_001127222.2	c.2974_2985delGAGGGCGAGGGC	p.Glu992_Gly995del	conservative_inframe_deletion	19/47	ENST00000360228.11	NP_001120694.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CACNA1A	ENST00000360228.11	c.2974_2985delGAGGGCGAGGGC	p.Glu992_Gly995del	conservative_inframe_deletion	19/47	1	NM_001127222.2	ENSP00000353362.5
CACNA1A	ENST00000638029.1	c.2986_2997delGAGGGCGAGGGC	p.Glu996_Gly999del	conservative_inframe_deletion	19/48	5		ENSP00000489829.1
CACNA1A	ENST00000573710.7	c.2980_2991delGAGGGCGAGGGC	p.Glu994_Gly997del	conservative_inframe_deletion	19/47	5		ENSP00000460092.3
CACNA1A	ENST00000635727.1	c.2977_2988delGAGGGCGAGGGC	p.Glu993_Gly996del	conservative_inframe_deletion	19/47	5		ENSP00000490001.1
CACNA1A	ENST00000637769.1	c.2977_2988delGAGGGCGAGGGC	p.Glu993_Gly996del	conservative_inframe_deletion	19/47	1		ENSP00000489778.1
CACNA1A	ENST00000636012.1	c.2977_2988delGAGGGCGAGGGC	p.Glu993_Gly996del	conservative_inframe_deletion	19/46	5		ENSP00000490223.1
CACNA1A	ENST00000637736.1	c.2836_2847delGAGGGCGAGGGC	p.Glu946_Gly949del	conservative_inframe_deletion	18/46	5		ENSP00000489861.1
CACNA1A	ENST00000636389.1	c.2977_2988delGAGGGCGAGGGC	p.Glu993_Gly996del	conservative_inframe_deletion	19/47	5		ENSP00000489992.1
CACNA1A	ENST00000637432.1	c.2986_2997delGAGGGCGAGGGC	p.Glu996_Gly999del	conservative_inframe_deletion	19/48	5		ENSP00000490617.1
CACNA1A	ENST00000636549.1	c.2977_2988delGAGGGCGAGGGC	p.Glu993_Gly996del	conservative_inframe_deletion	19/48	5		ENSP00000490578.1
CACNA1A	ENST00000637927.1	c.2980_2991delGAGGGCGAGGGC	p.Glu994_Gly997del	conservative_inframe_deletion	19/47	5		ENSP00000489715.1
CACNA1A	ENST00000635895.1	c.2977_2988delGAGGGCGAGGGC	p.Glu993_Gly996del	conservative_inframe_deletion	19/47	5		ENSP00000490323.1
CACNA1A	ENST00000638009.2	c.2977_2988delGAGGGCGAGGGC	p.Glu993_Gly996del	conservative_inframe_deletion	19/47	1		ENSP00000489913.1
CACNA1A	ENST00000637276.1	c.2977_2988delGAGGGCGAGGGC	p.Glu993_Gly996del	conservative_inframe_deletion	19/46	5		ENSP00000489777.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000513 AC: 7 AN: 1365414 Hom.: 0 AF XY: 0.00000446 AC XY: 3 AN XY: 673334

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000657

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

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

Uncertain significance, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Feb 22, 2020

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. Experimental studies and prediction algorithms are not available for this variant, and the functional significance of the deleted amino acids is currently unknown. This variant has not been reported in the literature in individuals with CACNA1A-related disease. While this variant is not present in population databases, the frequency information is unreliable, as metrics indicate poor data quality at this position in the ExAC database. This variant, c.2977_2988del, results in the deletion of 4 amino acids of the CACNA1A protein (p.Glu993_Gly996del), but otherwise preserves the integrity of the reading frame. -

not provided Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

GeneDx

May 04, 2021

Has not been previously published as pathogenic or benign to our knowledge; Not observed in large population cohorts (Lek et al., 2016); In-frame deletion of 4 amino acids in a non-repeat region; In silico analysis supports a deleterious effect on protein structure/function -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs764399373; hg19: chr19-13409461;