NM_021098.3:c.4120G>A

Variant names:

• chr16-1210868-G-A
• rs201855332
• NM_021098.3:c.4120G>A

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BS1_Supporting BS2

The NM_021098.3(CACNA1H):​c.4120G>A​(p.Val1374Met) variant causes a missense change. The variant allele was found at a frequency of 0.000338 in 1,605,478 control chromosomes in the GnomAD database, including 2 homozygotes. Variant has been reported in ClinVar as Uncertain significance (★★).

• Frequency:
  • Genomes: 𝑓 0.00018 (0 hom., cov: 35)
  • Exomes 𝑓: 0.00035 (2 hom.)
• Consequence: CACNA1H NM_021098.3 missense
• Clinical Significance: Uncertain significance criteria provided, multiple submitters, no conflicts U:3
• Conservation: PhyloP100: 6.60

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]

ACMG classification

Verdict is Likely_benign. Variant got -5 ACMG points.

• BS1: Variant frequency is greater than expected in population amr. gnomad4_exome allele frequency = 0.000354 (515/1453218) while in subpopulation AMR AF= 0.000559 (25/44716). AF 95% confidence interval is 0.000395. There are 2 homozygotes in gnomad4_exome. There are 227 alleles in male gnomad4_exome subpopulation. Median coverage is 39. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
• BS2: High AC in GnomAd4 at 27 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNA1H	NM_021098.3	c.4120G>A	p.Val1374Met	missense_variant	Exon 21 of 35	ENST00000348261.11	NP_066921.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CACNA1H	ENST00000348261.11	c.4120G>A	p.Val1374Met	missense_variant	Exon 21 of 35	1	NM_021098.3	ENSP00000334198.7
CACNA1H	ENST00000565831.6	c.4120G>A	p.Val1374Met	missense_variant	Exon 20 of 33	1		ENSP00000455840.1
CACNA1H	ENST00000638323.1	c.4081G>A	p.Val1361Met	missense_variant	Exon 21 of 35	5		ENSP00000492267.1
CACNA1H	ENST00000569107.5	c.343G>A	p.Val115Met	missense_variant	Exon 4 of 17	1		ENSP00000454990.2
CACNA1H	ENST00000564231.5	c.343G>A	p.Val115Met	missense_variant	Exon 4 of 18	1		ENSP00000457555.2
CACNA1H	ENST00000562079.5	c.343G>A	p.Val115Met	missense_variant	Exon 4 of 17	1		ENSP00000454581.2
CACNA1H	ENST00000637236.2	n.*90G>A		non_coding_transcript_exon_variant	Exon 5 of 6	5		ENSP00000492650.2
CACNA1H	ENST00000639478.1	n.4120G>A		non_coding_transcript_exon_variant	Exon 21 of 35	5		ENSP00000491945.1
CACNA1H	ENST00000640028.1	n.*2033G>A		non_coding_transcript_exon_variant	Exon 21 of 35	5		ENSP00000491488.1
CACNA1H	ENST00000637236.2	n.*90G>A		3_prime_UTR_variant	Exon 5 of 6	5		ENSP00000492650.2
CACNA1H	ENST00000640028.1	n.*2033G>A		3_prime_UTR_variant	Exon 21 of 35	5		ENSP00000491488.1

Frequencies

GnomAD3 genomes AF: 0.000177 AC: 27 AN: 152260 Hom.: 0 Cov.: 35

Gnomad AFR AF: 0.0000241

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000131

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000353

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.000279 AC: 68 AN: 243392 Hom.: 0 AF XY: 0.000218 AC XY: 29 AN XY: 132852

Gnomad AFR exome AF: 0.0000646

Gnomad AMR exome AF: 0.000609

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000357

Gnomad OTH exome AF: 0.00100

GnomAD4 exome AF: 0.000354 AC: 515 AN: 1453218 Hom.: 2 Cov.: 39 AF XY: 0.000314 AC XY: 227 AN XY: 723292

Gnomad4 AFR exome AF: 0.0000299

Gnomad4 AMR exome AF: 0.000559

Gnomad4 ASJ exome AF: 0.0000383

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.000427

Gnomad4 OTH exome AF: 0.000216

GnomAD4 genome AF: 0.000177 AC: 27 AN: 152260 Hom.: 0 Cov.: 35 AF XY: 0.000188 AC XY: 14 AN XY: 74390

Gnomad4 AFR AF: 0.0000241

Gnomad4 AMR AF: 0.000131

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000353

Gnomad4 OTH AF: 0.00

Alfa AF: 0.000501 Hom.: 0

Bravo AF: 0.000253

TwinsUK AF: 0.00 AC: 0

ALSPAC AF: 0.000778 AC: 3

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000233 AC: 2

ExAC AF: 0.000214 AC: 26

EpiCase AF: 0.000382

EpiControl AF: 0.000533

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:3

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not specified Uncertain:2

Jul 19, 2023

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: CACNA1H c.4120G>A (p.Val1374Met) results in a conservative amino acid change located in the Ion transport domain (IPR005821) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00028 in 243392 control chromosomes (gnomAD). To our knowledge, no occurrence of c.4120G>A in individuals affected with Idiopathic Generalized Epilepsy and no experimental evidence demonstrating its impact on protein function have been reported. Two submitters have cited clinical-significance assessments for this variant to ClinVar after 2014, and classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance. -

Jul 10, 2017

Athena Diagnostics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

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

Sep 27, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces valine, which is neutral and non-polar, with methionine, which is neutral and non-polar, at codon 1374 of the CACNA1H protein (p.Val1374Met). This variant is present in population databases (rs201855332, gnomAD 0.06%), and has an allele count higher than expected for a pathogenic variant. This variant has not been reported in the literature in individuals affected with CACNA1H-related conditions. ClinVar contains an entry for this variant (Variation ID: 446952). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is expected to disrupt CACNA1H protein function with a positive predictive value of 80%. 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	0.78
BayesDel_addAF	Uncertain	0.024	T
BayesDel_noAF	Pathogenic	0.16
CADD	Pathogenic	28
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.82	D;.;.;.
Eigen	Uncertain	0.67
Eigen_PC	Uncertain	0.64
FATHMM_MKL	Uncertain	0.96	D
LIST_S2	Uncertain	0.94	D;D;D;.
M_CAP	Uncertain	0.28	D
MetaRNN	Uncertain	0.56	D;D;D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Uncertain	2.3	M;.;M;M
PrimateAI	Uncertain	0.74	T
PROVEAN	Uncertain	-2.4	N;.;N;N
REVEL	Pathogenic	0.82
Sift	Uncertain	0.0010	D;.;D;D
Sift4G	Uncertain	0.0030	D;.;D;D
Polyphen		1.0	D;.;D;D
Vest4		0.71
MVP		0.94
ClinPred		0.22	T
GERP RS		4.2
Varity_R		0.66
gMVP		0.82

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: rs201855332; hg19: chr16-1260868;