16-1211178-C-T

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 4P and 4B. PM2PP3_ModerateBS2

The NM_021098.3(CACNA1H):c.4234C>T(p.Arg1412Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,460,434 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 variant affecting the same amino acid position, but resulting in a different missense (i.e. R1412Q) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 35)

Exomes 𝑓: 0.0000034 ( 0 hom. )

Consequence

CACNA1H
NM_021098.3 missense

Scores

Clinical Significance

Uncertain significance criteria provided, multiple submitters, no conflicts U:2

Conservation

PhyloP100: 2.13

Publications

1 publications found

Variant links:

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)

CACNA1H links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

PP3

MetaRNN computational evidence supports a deleterious effect, 0.909

BS2

High AC in GnomAdExome4 at 5 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNA1H	NM_021098.3 link	c.4234C>T	p.Arg1412Trp	missense_variant	Exon 22 of 35	ENST00000348261.11	NP_066921.2	O95180-1B3KQH9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
CACNA1H	ENST00000348261.11 link	c.4234C>T	p.Arg1412Trp	missense_variant	Exon 22 of 35	1	NM_021098.3	ENSP00000334198.7	O95180-1
CACNA1H	ENST00000569107.6 link	c.4234C>T	p.Arg1412Trp	missense_variant	Exon 22 of 34	1		ENSP00000454990.2	H3BNT0
CACNA1H	ENST00000711493.1 link	c.4234C>T	p.Arg1412Trp	missense_variant	Exon 22 of 34			ENSP00000518778.1
CACNA1H	ENST00000565831.7 link	c.4234C>T	p.Arg1412Trp	missense_variant	Exon 22 of 34	1		ENSP00000455840.1	O95180-2
CACNA1H	ENST00000711450.1 link	c.4234C>T	p.Arg1412Trp	missense_variant	Exon 22 of 35			ENSP00000518762.1
CACNA1H	ENST00000564231.6 link	c.4234C>T	p.Arg1412Trp	missense_variant	Exon 22 of 35	1		ENSP00000457555.2	H3BUA8
CACNA1H	ENST00000638323.1 link	c.4195C>T	p.Arg1399Trp	missense_variant	Exon 22 of 35	5		ENSP00000492267.1	A0A1W2PR14
CACNA1H	ENST00000562079.6 link	c.4234C>T	p.Arg1412Trp	missense_variant	Exon 22 of 34	1		ENSP00000454581.2	H3BMW6
CACNA1H	ENST00000711438.1 link	c.4195C>T	p.Arg1399Trp	missense_variant	Exon 22 of 34			ENSP00000518754.1
CACNA1H	ENST00000711482.1 link	c.4234C>T	p.Arg1412Trp	missense_variant	Exon 22 of 36			ENSP00000518771.1
CACNA1H	ENST00000711485.1 link	c.4234C>T	p.Arg1412Trp	missense_variant	Exon 22 of 35			ENSP00000518774.1
CACNA1H	ENST00000711455.1 link	c.4234C>T	p.Arg1412Trp	missense_variant	Exon 22 of 36			ENSP00000518768.1
CACNA1H	ENST00000711483.1 link	c.4234C>T	p.Arg1412Trp	missense_variant	Exon 22 of 35			ENSP00000518772.1
CACNA1H	ENST00000711456.1 link	c.4234C>T	p.Arg1412Trp	missense_variant	Exon 22 of 34			ENSP00000518769.1
CACNA1H	ENST00000621827.2 link	n.4234C>T		non_coding_transcript_exon_variant	Exon 22 of 37	6		ENSP00000518766.1
CACNA1H	ENST00000637236.3 link	n.*204C>T		non_coding_transcript_exon_variant	Exon 22 of 34	5		ENSP00000492650.2	A0A1W2PS38
CACNA1H	ENST00000639478.1 link	n.4234C>T		non_coding_transcript_exon_variant	Exon 22 of 35	5		ENSP00000491945.1	A0A1W2PQW2
CACNA1H	ENST00000640028.1 link	n.*2147C>T		non_coding_transcript_exon_variant	Exon 22 of 35	5		ENSP00000491488.1	A0A1W2PQ19
CACNA1H	ENST00000711442.1 link	n.*3681C>T		non_coding_transcript_exon_variant	Exon 21 of 34			ENSP00000518758.1
CACNA1H	ENST00000711448.1 link	n.4234C>T		non_coding_transcript_exon_variant	Exon 22 of 36			ENSP00000518760.1
CACNA1H	ENST00000711449.1 link	n.4234C>T		non_coding_transcript_exon_variant	Exon 22 of 35			ENSP00000518761.1
CACNA1H	ENST00000711451.1 link	n.4234C>T		non_coding_transcript_exon_variant	Exon 22 of 36			ENSP00000518763.1
CACNA1H	ENST00000711452.1 link	n.4234C>T		non_coding_transcript_exon_variant	Exon 22 of 36			ENSP00000518764.1
CACNA1H	ENST00000711453.1 link	n.4234C>T		non_coding_transcript_exon_variant	Exon 22 of 36			ENSP00000518765.1
CACNA1H	ENST00000711484.1 link	n.4234C>T		non_coding_transcript_exon_variant	Exon 22 of 35			ENSP00000518773.1
CACNA1H	ENST00000711486.1 link	n.4234C>T		non_coding_transcript_exon_variant	Exon 22 of 37			ENSP00000518775.1
CACNA1H	ENST00000711487.1 link	n.4234C>T		non_coding_transcript_exon_variant	Exon 22 of 36			ENSP00000518776.1
CACNA1H	ENST00000711488.1 link	n.4234C>T		non_coding_transcript_exon_variant	Exon 22 of 35			ENSP00000518777.1
CACNA1H	ENST00000637236.3 link	n.*204C>T		3_prime_UTR_variant	Exon 22 of 34	5		ENSP00000492650.2	A0A1W2PS38
CACNA1H	ENST00000640028.1 link	n.*2147C>T		3_prime_UTR_variant	Exon 22 of 35	5		ENSP00000491488.1	A0A1W2PQ19
CACNA1H	ENST00000711442.1 link	n.*3681C>T		3_prime_UTR_variant	Exon 21 of 34			ENSP00000518758.1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD2 exomes

AF:

0.00000403

AC:

AN:

247848

AF XY:

0.00

show subpopulations

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:

0.00

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000342

AC:

AN:

1460434

Hom.:

Cov.:

AF XY:

0.00000413

AC XY:

AN XY:

726508

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

33478

American (AMR)

AF:

0.00

AC:

AN:

44712

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

26132

East Asian (EAS)

AF:

0.00

AC:

AN:

39694

South Asian (SAS)

AF:

0.0000116

AC:

AN:

86250

European-Finnish (FIN)

AF:

0.00

AC:

AN:

52378

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5766

European-Non Finnish (NFE)

AF:

0.00000360

AC:

AN:

1111674

Other (OTH)

AF:

0.00

AC:

AN:

60350

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.455

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

Cov.:

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

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

Uncertain:1

Jun 04, 2024

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

Aug 14, 2020

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Uncertain significance

Review Status:criteria provided, single submitter

Collection Method:clinical testing

This sequence change replaces arginine with tryptophan at codon 1412 of the CACNA1H protein (p.Arg1412Trp). The arginine residue is highly conserved and there is a moderate physicochemical difference between arginine and tryptophan. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with CACNA1H-related disease. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. 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

0.51

BayesDel_noAF

Pathogenic

0.49

CADD

Pathogenic

(source)

DANN

Pathogenic

1.0

DEOGEN2

Pathogenic

0.93

D;.;.;.

Eigen

Uncertain

0.65

Eigen_PC

Uncertain

0.50

FATHMM_MKL

Uncertain

0.85

LIST_S2

Pathogenic

1.0

D;D;D;.

M_CAP

Pathogenic

0.35

MetaRNN

Pathogenic

0.91

D;D;D;D

MetaSVM

Pathogenic

1.1

MutationAssessor

Pathogenic

4.7

H;.;H;H

PhyloP100

2.1

PrimateAI

Pathogenic

0.91

PROVEAN

Pathogenic

-7.6

D;.;D;D

REVEL

Pathogenic

0.92

Sift

Pathogenic

0.0

D;.;D;D

Sift4G

Pathogenic

0.0

D;.;D;D

Polyphen

1.0

D;.;D;D

Vest4

0.80

MutPred

0.71

Loss of methylation at R1412 (P = 0.0112);.;Loss of methylation at R1412 (P = 0.0112);Loss of methylation at R1412 (P = 0.0112);

MVP

0.97

ClinPred

1.0

GERP RS

3.4

Varity_R

0.94

gMVP

0.92

Mutation Taster

=22/78

disease causing

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over