rs755221106

chr17-50617560-G-Achr17-50617560-G-T

Variant summary

Our verdict is Pathogenic. Variant got 15 ACMG points: 15P and 0B. PM2 PP2 PP3_Strong PP5_Very_Strong

The NM_018896.5(CACNA1G):c.5144G>A(p.Arg1715His) 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. 13/20 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: CACNA1G NM_018896.5 missense
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:7 O:1
• Conservation: PhyloP100: 10.0

Genes affected

CACNA1G (HGNC:1394): (calcium voltage-gated channel subunit alpha1 G) Voltage-sensitive 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, gene expression, cell motility, cell division, and cell death. This gene encodes a T-type, low-voltage activated calcium channel. The T-type channels generate currents that are both transient, owing to fast inactivation, and tiny, owing to small conductance. T-type channels are thought to be involved in pacemaker activity, low-threshold calcium spikes, neuronal oscillations and resonance, and rebound burst firing. Many alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Sep 2011]

ACMG classification

Verdict is Pathogenic. Variant got 15 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP2: Missense variant where missense usually causes diseases, CACNA1G
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.976
• PP5: Variant 17-50617560-G-A is Pathogenic according to our data. Variant chr17-50617560-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 221981.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CACNA1G	NM_018896.5	c.5144G>A	p.Arg1715His	missense_variant	29/38	ENST00000359106.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CACNA1G	ENST00000359106.10	c.5144G>A	p.Arg1715His	missense_variant	29/38	1	NM_018896.5	A2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:7 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Spinocerebellar ataxia type 42 Pathogenic:4

Pathogenic, criteria provided, single submitter	clinical testing	Genetics and Molecular Pathology, SA Pathology	Aug 05, 2021	The CACNA1G c. 5144G>A variant is classified as a PATHOGENIC variant (PS4, PS3, PP1_Strong, PP3, PP5) The variant is a single nucleotide change from a guanine to an adenine at position 5144 which is predicted to change the Arginine at position 1715 in the protein to Histidine. The variant is in exon 29 and is located in protein domains: ion transport domain, and Polycystin cation channel, of the CACNA1G gene. This variant is a recurrent pathogenic variant in the CACNA1G gene, and it has been previously reported in many individuals with Cerebellar ataxias in heterozygoys state (PMID: 26456284, 26715324, 28490766, 29629410) (PS4). This variant is in dbSNP (rs755221106) but is absent from population databases. In vitro functonal studies have demonstrated that this variant had resulted in a significant shift of the steady-state activation curve towards more positive membrane potential values, whereas the inactivation curve had a higher slope factor, supporting the damaging effect on the gene or gene product (PMID: 26456284, 26715324) (PS3). Multiple pedigrees of Cerebellar ataxia-affected families with this variant has been previously reported showing segregation of this variant with the disorder (PMID: PMID: 26456284, 26715324, 28490766, 29629410) (PP1_Strong). The variant has been reported in the ClinVar (Variation ID: 221981) and HGMD (Accession: CM1511857) as Pathogenic (PP5). Computational predictions support a deleterious effect on the gene or gene product (PP3). -
Pathogenic, no assertion criteria provided	literature only	OMIM	Aug 14, 2018	- -
Pathogenic, criteria provided, single submitter	research	Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Fondazione Stella Maris	Jan 04, 2021	- -
Pathogenic, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Jun 02, 2016	- -

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	May 13, 2022	Published functional studies demonstrate a damaging effect on membrane potential dependency (Coutelier et al., 2015; Morino et al., 2015); 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; This variant is associated with the following publications: (PMID: 29915382, 34426522, 30200108, 29474447, 35054808, 29421541, 31892274, 30842224, 32878331, 32638069, 34248568, 31999455, 34220096, 33746731, 31229688, 33243296, 31836334, 28490766, 26715324, 33624863, 31692161, 26456284, 29629410, 33163565, 31217264) -
Pathogenic, criteria provided, single submitter	clinical testing	Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen	Oct 23, 2020	- -

Spinocerebellar ataxia type 42;C4748120:Spinocerebellar ataxia 42, early-onset, severe, with neurodevelopmental deficits Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Oct 31, 2018

- -

CACNA1G-related disorders Other:1

not provided, no classification provided

phenotyping only

GenomeConnect, ClinGen

-

GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.99
BayesDel_addAF	Pathogenic	0.59	D
BayesDel_noAF	Pathogenic	0.60
Cadd	Pathogenic	34
Dann	Pathogenic	1.0
Eigen	Pathogenic	1.1
Eigen_PC	Pathogenic	1.0
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Pathogenic	1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
M_CAP	Pathogenic	0.87	D
MetaRNN	Pathogenic	0.98	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM	Pathogenic	0.99	D
MutationTaster	Benign	1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
PrimateAI	Pathogenic	0.93	D
PROVEAN	Pathogenic	-4.9	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
REVEL	Pathogenic	0.94
Sift	Pathogenic	0.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
Sift4G	Pathogenic	0.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
Polyphen		1.0	.;.;.;.;D;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;D;.
Vest4		0.83
MutPred		0.85		.;.;.;.;.;.;.;.;.;.;Loss of MoRF binding (P = 0.0487);.;.;Loss of MoRF binding (P = 0.0487);.;Loss of MoRF binding (P = 0.0487);.;.;.;.;Loss of MoRF binding (P = 0.0487);.;.;Loss of MoRF binding (P = 0.0487);.;
MVP		0.99
MPC		2.6
ClinPred		1.0	D
GERP RS		5.0
Varity_R		0.96
gMVP		0.99

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: rs755221106; hg19: chr17-48694921;