NM_001127222.2:c.5986A>G

Variant names:

• chr19-13212695-T-C
• rs141963371
• NM_001127222.2:c.5986A>G

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 1P and 7B. PP2 BP4_Moderate BP6 BS2

The NM_001127222.2(CACNA1A):​c.5986A>G​(p.Thr1996Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000543 in 1,510,702 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

• Frequency:
  • Genomes: 𝑓 0.000046 (0 hom., cov: 32)
  • Exomes 𝑓: 0.000055 (0 hom.)
• Consequence: CACNA1A NM_001127222.2 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:3 B:2
• Conservation: PhyloP100: 1.40

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 -6 ACMG points.

• PP2: Missense variant in the CACNA1A gene, where missense mutations are typically associated with disease (based on misZ statistic). The gene has 137 curated pathogenic missense variants (we use a threshold of 10). The gene has 132 curated benign missense variants. Gene score misZ: 5.7845 (above the threshold of 3.09). Trascript score misZ: 3.9354 (above the threshold of 3.09). GenCC associations: The gene is linked to 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.
• BP4: Computational evidence support a benign effect (MetaRNN=0.084127486).
• BP6: Variant 19-13212695-T-C is Benign according to our data. Variant chr19-13212695-T-C is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 450300.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=2, Uncertain_significance=3}.
• BS2: High AC in GnomAd4 at 7 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNA1A	NM_001127222.2	c.5986A>G	p.Thr1996Ala	missense_variant	Exon 41 of 47	ENST00000360228.11	NP_001120694.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CACNA1A	ENST00000360228.11	c.5986A>G	p.Thr1996Ala	missense_variant	Exon 41 of 47	1	NM_001127222.2	ENSP00000353362.5
CACNA1A	ENST00000638029.1	c.6004A>G	p.Thr2002Ala	missense_variant	Exon 42 of 48	5		ENSP00000489829.1
CACNA1A	ENST00000573710.7	c.5992A>G	p.Thr1998Ala	missense_variant	Exon 41 of 47	5		ENSP00000460092.3
CACNA1A	ENST00000635727.1	c.5989A>G	p.Thr1997Ala	missense_variant	Exon 41 of 47	5		ENSP00000490001.1
CACNA1A	ENST00000637769.1	c.5989A>G	p.Thr1997Ala	missense_variant	Exon 41 of 47	1		ENSP00000489778.1
CACNA1A	ENST00000636012.1	c.5989A>G	p.Thr1997Ala	missense_variant	Exon 41 of 46	5		ENSP00000490223.1
CACNA1A	ENST00000637736.1	c.5848A>G	p.Thr1950Ala	missense_variant	Exon 40 of 46	5		ENSP00000489861.1
CACNA1A	ENST00000636389.1	c.5989A>G	p.Thr1997Ala	missense_variant	Exon 41 of 47	5		ENSP00000489992.1
CACNA1A	ENST00000637432.1	c.6004A>G	p.Thr2002Ala	missense_variant	Exon 42 of 48	5		ENSP00000490617.1
CACNA1A	ENST00000636549.1	c.5995A>G	p.Thr1999Ala	missense_variant	Exon 42 of 48	5		ENSP00000490578.1
CACNA1A	ENST00000637927.1	c.5992A>G	p.Thr1998Ala	missense_variant	Exon 41 of 47	5		ENSP00000489715.1
CACNA1A	ENST00000635895.1	c.5989A>G	p.Thr1997Ala	missense_variant	Exon 41 of 47	5		ENSP00000490323.1
CACNA1A	ENST00000638009.2	c.5989A>G	p.Thr1997Ala	missense_variant	Exon 41 of 47	1		ENSP00000489913.1
CACNA1A	ENST00000637276.1	c.5989A>G	p.Thr1997Ala	missense_variant	Exon 41 of 46	5		ENSP00000489777.1
CACNA1A	ENST00000636768.1	n.*288A>G		non_coding_transcript_exon_variant	Exon 6 of 10	5		ENSP00000490190.2
CACNA1A	ENST00000636768.1	n.*288A>G		3_prime_UTR_variant	Exon 6 of 10	5		ENSP00000490190.2

Frequencies

GnomAD3 genomes AF: 0.0000461 AC: 7 AN: 151990 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.0000242

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000416

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0000441

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000489 AC: 8 AN: 163620 Hom.: 0 AF XY: 0.0000462 AC XY: 4 AN XY: 86494

Gnomad AFR exome AF: 0.0000762

Gnomad AMR exome AF: 0.0000498

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.0000756

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000623

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000552 AC: 75 AN: 1358594 Hom.: 0 Cov.: 33 AF XY: 0.0000572 AC XY: 38 AN XY: 664366

Gnomad4 AFR exome AF: 0.0000663

Gnomad4 AMR exome AF: 0.0000696

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000723

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000593

Gnomad4 OTH exome AF: 0.0000358

GnomAD4 genome AF: 0.0000460 AC: 7 AN: 152108 Hom.: 0 Cov.: 32 AF XY: 0.0000672 AC XY: 5 AN XY: 74358

Gnomad4 AFR AF: 0.0000241

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.000416

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000441

Gnomad4 OTH AF: 0.00

Bravo AF: 0.0000529

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000361 AC: 3

ExAC AF: 0.0000686 AC: 8

Asia WGS AF: 0.000289 AC: 1 AN: 3478

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:3 Benign:2

Revision: criteria provided, conflicting classifications

Submissions by phenotype

not provided Uncertain:2 Benign:1

Jan 29, 2019

Athena Diagnostics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Dec 16, 2020

GeneDx

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Feb 01, 2023

CeGaT Center for Human Genetics Tuebingen

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

CACNA1A: PP2 -

Inborn genetic diseases Uncertain:1

Aug 02, 2021

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.5989A>G (p.T1997A) alteration is located in exon 41 (coding exon 41) of the CACNA1A gene. This alteration results from a A to G substitution at nucleotide position 5989, causing the threonine (T) at amino acid position 1997 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

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

May 08, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.074
BayesDel_addAF	Benign	-0.062	T
BayesDel_noAF	Benign	-0.14
CADD	Benign	21
DANN	Benign	0.53
DEOGEN2	Benign	0.019	.;.;T;.;.;.;.;.;T;.;.;T;.;.;.;T;.;.
Eigen	Benign	-0.75
Eigen_PC	Benign	-0.72
FATHMM_MKL	Uncertain	0.83	D
LIST_S2	Benign	0.77	T;T;T;T;T;T;T;T;T;T;.;T;T;T;T;T;T;T
M_CAP	Uncertain	0.11	D
MetaRNN	Benign	0.084	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM	Uncertain	-0.085	T
MutationAssessor	Benign	1.9	.;.;.;.;L;.;.;.;.;.;.;.;.;.;L;.;.;.
PrimateAI	Uncertain	0.59	T
PROVEAN	Benign	-2.0	.;N;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.
REVEL	Benign	0.25
Sift	Benign	0.63	.;T;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.
Sift4G	Benign	0.57	T;T;.;.;.;T;.;.;.;.;.;.;.;.;.;.;.;.
Vest4		0.31
MVP		0.86
MPC		0.47
ClinPred		0.029	T
GERP RS		3.3
Varity_R		0.11
gMVP		0.13

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: rs141963371; hg19: chr19-13323509; COSMIC: COSV64198896; COSMIC: COSV64198896;