NM_021098.3:c.489G>T

Variant names:

• chr16-1195509-G-T
• rs60593994
• NM_021098.3:c.489G>T

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2 BP4

The NM_021098.3(CACNA1H):​c.489G>T​(p.Gln163His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000689 in 1,450,554 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Benign in ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q163P) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: CACNA1H NM_021098.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.63
• Publications: 0 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: Uncertain_significance. The variant received 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.41852993).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNA1H	NM_021098.3	c.489G>T	p.Gln163His	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.489G>T	p.Gln163His	missense_variant	Exon 4 of 35	1	NM_021098.3	ENSP00000334198.7
CACNA1H	ENST00000569107.6	c.489G>T	p.Gln163His	missense_variant	Exon 4 of 34	1		ENSP00000454990.2
CACNA1H	ENST00000711493.1	c.489G>T	p.Gln163His	missense_variant	Exon 4 of 34			ENSP00000518778.1
CACNA1H	ENST00000565831.7	c.489G>T	p.Gln163His	missense_variant	Exon 4 of 34	1		ENSP00000455840.1
CACNA1H	ENST00000711450.1	c.489G>T	p.Gln163His	missense_variant	Exon 4 of 35			ENSP00000518762.1
CACNA1H	ENST00000564231.6	c.489G>T	p.Gln163His	missense_variant	Exon 4 of 35	1		ENSP00000457555.2
CACNA1H	ENST00000638323.1	c.450G>T	p.Gln150His	missense_variant	Exon 4 of 35	5		ENSP00000492267.1
CACNA1H	ENST00000562079.6	c.489G>T	p.Gln163His	missense_variant	Exon 4 of 34	1		ENSP00000454581.2
CACNA1H	ENST00000711438.1	c.450G>T	p.Gln150His	missense_variant	Exon 4 of 34			ENSP00000518754.1
CACNA1H	ENST00000711482.1	c.489G>T	p.Gln163His	missense_variant	Exon 4 of 36			ENSP00000518771.1
CACNA1H	ENST00000711485.1	c.489G>T	p.Gln163His	missense_variant	Exon 4 of 35			ENSP00000518774.1
CACNA1H	ENST00000711455.1	c.489G>T	p.Gln163His	missense_variant	Exon 4 of 36			ENSP00000518768.1
CACNA1H	ENST00000711483.1	c.489G>T	p.Gln163His	missense_variant	Exon 4 of 35			ENSP00000518772.1
CACNA1H	ENST00000711456.1	c.489G>T	p.Gln163His	missense_variant	Exon 4 of 34			ENSP00000518769.1
CACNA1H	ENST00000621827.2	n.489G>T		non_coding_transcript_exon_variant	Exon 4 of 37	6		ENSP00000518766.1
CACNA1H	ENST00000637236.3	n.489G>T		non_coding_transcript_exon_variant	Exon 4 of 34	5		ENSP00000492650.2
CACNA1H	ENST00000639478.1	n.489G>T		non_coding_transcript_exon_variant	Exon 4 of 35	5		ENSP00000491945.1
CACNA1H	ENST00000640028.1	n.489G>T		non_coding_transcript_exon_variant	Exon 4 of 35	5		ENSP00000491488.1
CACNA1H	ENST00000711442.1	n.489G>T		non_coding_transcript_exon_variant	Exon 4 of 34			ENSP00000518758.1
CACNA1H	ENST00000711448.1	n.489G>T		non_coding_transcript_exon_variant	Exon 4 of 36			ENSP00000518760.1
CACNA1H	ENST00000711449.1	n.489G>T		non_coding_transcript_exon_variant	Exon 4 of 35			ENSP00000518761.1
CACNA1H	ENST00000711451.1	n.489G>T		non_coding_transcript_exon_variant	Exon 4 of 36			ENSP00000518763.1
CACNA1H	ENST00000711452.1	n.489G>T		non_coding_transcript_exon_variant	Exon 4 of 36			ENSP00000518764.1
CACNA1H	ENST00000711453.1	n.489G>T		non_coding_transcript_exon_variant	Exon 4 of 36			ENSP00000518765.1
CACNA1H	ENST00000711484.1	n.489G>T		non_coding_transcript_exon_variant	Exon 4 of 35			ENSP00000518773.1
CACNA1H	ENST00000711486.1	n.489G>T		non_coding_transcript_exon_variant	Exon 4 of 37			ENSP00000518775.1
CACNA1H	ENST00000711487.1	n.489G>T		non_coding_transcript_exon_variant	Exon 4 of 36			ENSP00000518776.1
CACNA1H	ENST00000711488.1	n.489G>T		non_coding_transcript_exon_variant	Exon 4 of 35			ENSP00000518777.1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 6.89e-7 AC: 1 AN: 1450554 Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0 AN XY: 720220

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 33312

American (AMR) AF: 0.00 AC: 0 AN: 43162

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 25910

East Asian (EAS) AF: 0.0000255 AC: 1 AN: 39228

South Asian (SAS) AF: 0.00 AC: 0 AN: 83766

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 52536

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5710

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 1106932

Other (OTH) AF: 0.00 AC: 0 AN: 59998

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.28
BayesDel_addAF	Pathogenic	0.18	D
BayesDel_noAF	Uncertain	0.020
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Uncertain	0.58	D;.;.;.
Eigen	Benign	-0.093
Eigen_PC	Benign	-0.034
FATHMM_MKL	Uncertain	0.77	D
LIST_S2	Uncertain	0.87	D;D;D;.
M_CAP	Pathogenic	0.36	D
MetaRNN	Benign	0.42	T;T;T;T
MetaSVM	Uncertain	0.61	D
MutationAssessor	Benign	0.76	N;.;N;N
PhyloP100		1.6
PrimateAI	Uncertain	0.54	T
PROVEAN	Benign	-2.3	N;.;N;N
REVEL	Uncertain	0.58
Sift	Benign	0.061	T;.;T;T
Sift4G	Uncertain	0.028	D;.;D;D
Polyphen		0.051	B;.;D;D
Vest4		0.49
MutPred		0.49		Loss of helix (P = 0.028);.;Loss of helix (P = 0.028);Loss of helix (P = 0.028);
MVP		0.91
ClinPred		0.85	D
GERP RS		2.7
Varity_R		0.33
gMVP		0.61
Mutation Taster		=96/4	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: rs60593994; hg19: chr16-1245509;