rs1052743921

Variant names:

• chr16-1153780-C-A
• rs1052743921
• NM_021098.3:c.43C>A

Your query was ambiguous. Multiple possible variants found:

• chr16-1153780-C-A
• chr16-1153780-C-T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_021098.3(CACNA1H):​c.43C>A​(p.Leu15Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000929 in 1,076,310 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. Synonymous variant affecting the same amino acid position (i.e. L15L) has been classified as Likely benign.

• Frequency:
  • Genomes: not found (cov: 31)
  • Exomes 𝑓: 9.3e-7 (0 hom.)
• Consequence: CACNA1H NM_021098.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.450
• 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 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.24185312).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CACNA1H	NM_021098.3	c.43C>A	p.Leu15Met	missense_variant	Exon 2 of 35	ENST00000348261.11	NP_066921.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CACNA1H	ENST00000348261.11	c.43C>A	p.Leu15Met	missense_variant	Exon 2 of 35	1	NM_021098.3	ENSP00000334198.7
CACNA1H	ENST00000569107.6	c.43C>A	p.Leu15Met	missense_variant	Exon 2 of 34	1		ENSP00000454990.2
CACNA1H	ENST00000711493.1	c.43C>A	p.Leu15Met	missense_variant	Exon 2 of 34			ENSP00000518778.1
CACNA1H	ENST00000565831.7	c.43C>A	p.Leu15Met	missense_variant	Exon 2 of 34	1		ENSP00000455840.1
CACNA1H	ENST00000711450.1	c.43C>A	p.Leu15Met	missense_variant	Exon 2 of 35			ENSP00000518762.1
CACNA1H	ENST00000564231.6	c.43C>A	p.Leu15Met	missense_variant	Exon 2 of 35	1		ENSP00000457555.2
CACNA1H	ENST00000638323.1	c.43C>A	p.Leu15Met	missense_variant	Exon 2 of 35	5		ENSP00000492267.1
CACNA1H	ENST00000562079.6	c.43C>A	p.Leu15Met	missense_variant	Exon 2 of 34	1		ENSP00000454581.2
CACNA1H	ENST00000711438.1	c.43C>A	p.Leu15Met	missense_variant	Exon 2 of 34			ENSP00000518754.1
CACNA1H	ENST00000711482.1	c.43C>A	p.Leu15Met	missense_variant	Exon 2 of 36			ENSP00000518771.1
CACNA1H	ENST00000711485.1	c.43C>A	p.Leu15Met	missense_variant	Exon 2 of 35			ENSP00000518774.1
CACNA1H	ENST00000711455.1	c.43C>A	p.Leu15Met	missense_variant	Exon 2 of 36			ENSP00000518768.1
CACNA1H	ENST00000711483.1	c.43C>A	p.Leu15Met	missense_variant	Exon 2 of 35			ENSP00000518772.1
CACNA1H	ENST00000711456.1	c.43C>A	p.Leu15Met	missense_variant	Exon 2 of 34			ENSP00000518769.1
CACNA1H	ENST00000621827.2	n.43C>A		non_coding_transcript_exon_variant	Exon 2 of 37	6		ENSP00000518766.1
CACNA1H	ENST00000637236.3	n.43C>A		non_coding_transcript_exon_variant	Exon 2 of 34	5		ENSP00000492650.2
CACNA1H	ENST00000639478.1	n.43C>A		non_coding_transcript_exon_variant	Exon 2 of 35	5		ENSP00000491945.1
CACNA1H	ENST00000640028.1	n.43C>A		non_coding_transcript_exon_variant	Exon 2 of 35	5		ENSP00000491488.1
CACNA1H	ENST00000711442.1	n.43C>A		non_coding_transcript_exon_variant	Exon 2 of 34			ENSP00000518758.1
CACNA1H	ENST00000711448.1	n.43C>A		non_coding_transcript_exon_variant	Exon 2 of 36			ENSP00000518760.1
CACNA1H	ENST00000711449.1	n.43C>A		non_coding_transcript_exon_variant	Exon 2 of 35			ENSP00000518761.1
CACNA1H	ENST00000711451.1	n.43C>A		non_coding_transcript_exon_variant	Exon 2 of 36			ENSP00000518763.1
CACNA1H	ENST00000711452.1	n.43C>A		non_coding_transcript_exon_variant	Exon 2 of 36			ENSP00000518764.1
CACNA1H	ENST00000711453.1	n.43C>A		non_coding_transcript_exon_variant	Exon 2 of 36			ENSP00000518765.1
CACNA1H	ENST00000711484.1	n.43C>A		non_coding_transcript_exon_variant	Exon 2 of 35			ENSP00000518773.1
CACNA1H	ENST00000711486.1	n.43C>A		non_coding_transcript_exon_variant	Exon 2 of 37			ENSP00000518775.1
CACNA1H	ENST00000711487.1	n.43C>A		non_coding_transcript_exon_variant	Exon 2 of 36			ENSP00000518776.1
CACNA1H	ENST00000711488.1	n.43C>A		non_coding_transcript_exon_variant	Exon 2 of 35			ENSP00000518777.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 9.29e-7 AC: 1 AN: 1076310 Hom.: 0 Cov.: 32 AF XY: 0.00000196 AC XY: 1 AN XY: 510682

African (AFR) AF: 0.00 AC: 0 AN: 22004

American (AMR) AF: 0.00 AC: 0 AN: 7636

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 13370

East Asian (EAS) AF: 0.00 AC: 0 AN: 24236

South Asian (SAS) AF: 0.00 AC: 0 AN: 24690

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 21758

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2822

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 917210

Other (OTH) AF: 0.0000235 AC: 1 AN: 42584

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.23
BayesDel_addAF	Uncertain	0.071	D
BayesDel_noAF	Benign	-0.14
CADD	Uncertain	24
DANN	Uncertain	0.99
DEOGEN2	Benign	0.098	T;.;.;.
Eigen	Benign	-0.37
Eigen_PC	Benign	-0.43
FATHMM_MKL	Benign	0.034	N
LIST_S2	Benign	0.48	T;T;T;.
M_CAP	Pathogenic	0.94	D
MetaRNN	Benign	0.24	T;T;T;T
MetaSVM	Uncertain	0.11	D
MutationAssessor	Benign	1.4	L;.;L;L
PhyloP100		0.45
PrimateAI	Pathogenic	0.88	D
PROVEAN	Benign	-0.070	N;.;N;N
REVEL	Benign	0.22
Sift	Uncertain	0.018	D;.;D;D
Sift4G	Uncertain	0.053	T;.;T;T
Polyphen		0.84	P;.;P;P
Vest4		0.24
MutPred		0.26		Gain of catalytic residue at V11 (P = 0.0174);Gain of catalytic residue at V11 (P = 0.0174);Gain of catalytic residue at V11 (P = 0.0174);Gain of catalytic residue at V11 (P = 0.0174);
MVP		0.78
ClinPred		0.52	D
GERP RS		1.8
PromoterAI		0.0037	Neutral
Varity_R		0.14
gMVP		0.23
Mutation Taster		=89/11	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: rs1052743921; hg19: chr16-1203780;