NM_021098.3:c.483C>G

Variant names:

• chr16-1195503-C-G
• rs119454947
• NM_021098.3:c.483C>G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PP3_Moderate BS2

The NM_021098.3(CACNA1H):​c.483C>G​(p.Phe161Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000193 in 1,448,276 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 (★★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar. Synonymous variant affecting the same amino acid position (i.e. F161F) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.000019 (0 hom.)
• Consequence: CACNA1H NM_021098.3 missense
• Clinical Significance: Uncertain significance criteria provided, multiple submitters, no conflicts U:2
• Conservation: PhyloP100: -1.04
• Publications: 7 publications found

Genes affected

CACNA1H (HGNC:1395): (calcium voltage-gated channel subunit alpha1 H) This gene encodes a T-type member of the alpha-1 subunit family, a protein in the voltage-dependent calcium channel complex. Calcium channels mediate the influx of calcium ions into the cell upon membrane polarization and consist of a complex of alpha-1, alpha-2/delta, beta, and gamma subunits in a 1:1:1:1 ratio. The alpha-1 subunit has 24 transmembrane segments and forms the pore through which ions pass into the cell. There are multiple isoforms of each of the proteins in the complex, either encoded by different genes or the result of alternative splicing of transcripts. Alternate transcriptional splice variants, encoding different isoforms, have been characterized for the gene described here. Studies suggest certain mutations in this gene lead to childhood absence epilepsy (CAE). [provided by RefSeq, Jul 2008]

CACNA1H Gene-Disease associations (from GenCC):

• hyperaldosteronism, familial, type IV

  Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• childhood absence epilepsy

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
• epilepsy, childhood absence, susceptibility to, 6

  Inheritance: AD Classification: LIMITED Submitted by: G2P, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PP3: MetaRNN computational evidence supports a deleterious effect, 0.919
• BS2: High AC in GnomAdExome4 at 28 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNA1H	NM_021098.3	c.483C>G	p.Phe161Leu	missense_variant	Exon 4 of 35	ENST00000348261.11	NP_066921.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CACNA1H	ENST00000348261.11	c.483C>G	p.Phe161Leu	missense_variant	Exon 4 of 35	1	NM_021098.3	ENSP00000334198.7
CACNA1H	ENST00000569107.6	c.483C>G	p.Phe161Leu	missense_variant	Exon 4 of 34	1		ENSP00000454990.2
CACNA1H	ENST00000711493.1	c.483C>G	p.Phe161Leu	missense_variant	Exon 4 of 34			ENSP00000518778.1
CACNA1H	ENST00000565831.7	c.483C>G	p.Phe161Leu	missense_variant	Exon 4 of 34	1		ENSP00000455840.1
CACNA1H	ENST00000711450.1	c.483C>G	p.Phe161Leu	missense_variant	Exon 4 of 35			ENSP00000518762.1
CACNA1H	ENST00000564231.6	c.483C>G	p.Phe161Leu	missense_variant	Exon 4 of 35	1		ENSP00000457555.2
CACNA1H	ENST00000638323.1	c.444C>G	p.Phe148Leu	missense_variant	Exon 4 of 35	5		ENSP00000492267.1
CACNA1H	ENST00000562079.6	c.483C>G	p.Phe161Leu	missense_variant	Exon 4 of 34	1		ENSP00000454581.2
CACNA1H	ENST00000711438.1	c.444C>G	p.Phe148Leu	missense_variant	Exon 4 of 34			ENSP00000518754.1
CACNA1H	ENST00000711482.1	c.483C>G	p.Phe161Leu	missense_variant	Exon 4 of 36			ENSP00000518771.1
CACNA1H	ENST00000711485.1	c.483C>G	p.Phe161Leu	missense_variant	Exon 4 of 35			ENSP00000518774.1
CACNA1H	ENST00000711455.1	c.483C>G	p.Phe161Leu	missense_variant	Exon 4 of 36			ENSP00000518768.1
CACNA1H	ENST00000711483.1	c.483C>G	p.Phe161Leu	missense_variant	Exon 4 of 35			ENSP00000518772.1
CACNA1H	ENST00000711456.1	c.483C>G	p.Phe161Leu	missense_variant	Exon 4 of 34			ENSP00000518769.1
CACNA1H	ENST00000621827.2	n.483C>G		non_coding_transcript_exon_variant	Exon 4 of 37	6		ENSP00000518766.1
CACNA1H	ENST00000637236.3	n.483C>G		non_coding_transcript_exon_variant	Exon 4 of 34	5		ENSP00000492650.2
CACNA1H	ENST00000639478.1	n.483C>G		non_coding_transcript_exon_variant	Exon 4 of 35	5		ENSP00000491945.1
CACNA1H	ENST00000640028.1	n.483C>G		non_coding_transcript_exon_variant	Exon 4 of 35	5		ENSP00000491488.1
CACNA1H	ENST00000711442.1	n.483C>G		non_coding_transcript_exon_variant	Exon 4 of 34			ENSP00000518758.1
CACNA1H	ENST00000711448.1	n.483C>G		non_coding_transcript_exon_variant	Exon 4 of 36			ENSP00000518760.1
CACNA1H	ENST00000711449.1	n.483C>G		non_coding_transcript_exon_variant	Exon 4 of 35			ENSP00000518761.1
CACNA1H	ENST00000711451.1	n.483C>G		non_coding_transcript_exon_variant	Exon 4 of 36			ENSP00000518763.1
CACNA1H	ENST00000711452.1	n.483C>G		non_coding_transcript_exon_variant	Exon 4 of 36			ENSP00000518764.1
CACNA1H	ENST00000711453.1	n.483C>G		non_coding_transcript_exon_variant	Exon 4 of 36			ENSP00000518765.1
CACNA1H	ENST00000711484.1	n.483C>G		non_coding_transcript_exon_variant	Exon 4 of 35			ENSP00000518773.1
CACNA1H	ENST00000711486.1	n.483C>G		non_coding_transcript_exon_variant	Exon 4 of 37			ENSP00000518775.1
CACNA1H	ENST00000711487.1	n.483C>G		non_coding_transcript_exon_variant	Exon 4 of 36			ENSP00000518776.1
CACNA1H	ENST00000711488.1	n.483C>G		non_coding_transcript_exon_variant	Exon 4 of 35			ENSP00000518777.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD2 exomes AF: 0.00000881 AC: 2 AN: 227114 AF XY: 0.00

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: 0.0000196

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000193 AC: 28 AN: 1448276 Hom.: 0 Cov.: 34 AF XY: 0.0000139 AC XY: 10 AN XY: 718856

African (AFR) AF: 0.0000301 AC: 1 AN: 33266

American (AMR) AF: 0.0000234 AC: 1 AN: 42782

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25868

East Asian (EAS) AF: 0.00 AC: 0 AN: 39100

South Asian (SAS) AF: 0.00 AC: 0 AN: 83462

European-Finnish (FIN) AF: 0.0000191 AC: 1 AN: 52446

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5716

European-Non Finnish (NFE) AF: 0.0000217 AC: 24 AN: 1105714

Other (OTH) AF: 0.0000167 AC: 1 AN: 59922

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

ExAC AF: 0.0000166 AC: 2

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Epilepsy, childhood absence, susceptibility to, 6;C4310756:Hyperaldosteronism, familial, type IV Uncertain:1

Sep 25, 2021

Fulgent Genetics, Fulgent Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Idiopathic generalized epilepsy;C4310756:Hyperaldosteronism, familial, type IV Uncertain:1

Mar 29, 2021

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces phenylalanine with leucine at codon 161 of the CACNA1H protein (p.Phe161Leu). The phenylalanine residue is highly conserved and there is a small physicochemical difference between phenylalanine and leucine. This variant is present in population databases (rs119454947, ExAC 0.008%). This missense change has been observed in individual(s) with childhood absence epilepsy (PMID: 12891677). 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 CACNA1H protein function. 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. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.94
BayesDel_addAF	Pathogenic	0.29	D
BayesDel_noAF	Pathogenic	0.20
CADD	Benign	19
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.77	D;.;.;.
Eigen	Benign	-0.28
Eigen_PC	Benign	-0.48
FATHMM_MKL	Benign	0.13	N
LIST_S2	Uncertain	0.93	D;D;D;.
M_CAP	Pathogenic	0.46	D
MetaRNN	Pathogenic	0.92	D;D;D;D
MetaSVM	Uncertain	0.78	D
MutationAssessor	Benign	1.4	L;.;L;L
PhyloP100		-1.0
PrimateAI	Uncertain	0.78	T
PROVEAN	Pathogenic	-5.0	D;.;D;D
REVEL	Uncertain	0.64
Sift	Benign	0.087	T;.;T;T
Sift4G	Uncertain	0.014	D;.;D;D
Polyphen		0.98	D;.;D;D
Vest4		0.78
MutPred		0.87		Loss of loop (P = 0.1242);.;Loss of loop (P = 0.1242);Loss of loop (P = 0.1242);
MVP		1.0
ClinPred		0.99	D
GERP RS		-4.3
Varity_R		0.35
gMVP		0.59
Mutation Taster		=79/21	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: rs119454947; hg19: chr16-1245503;