rs754671059
Positions:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_021098.3(CACNA1H):āc.3931A>Gā(p.Ile1311Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000118 in 1,610,738 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.000053 ( 0 hom., cov: 27)
Exomes š: 0.0000075 ( 0 hom. )
Consequence
CACNA1H
NM_021098.3 missense
NM_021098.3 missense
Scores
2
12
5
Clinical Significance
Conservation
PhyloP100: 7.33
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]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
BS2
High AC in GnomAd4 at 8 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CACNA1H | NM_021098.3 | c.3931A>G | p.Ile1311Val | missense_variant | 19/35 | ENST00000348261.11 | NP_066921.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CACNA1H | ENST00000348261.11 | c.3931A>G | p.Ile1311Val | missense_variant | 19/35 | 1 | NM_021098.3 | ENSP00000334198.7 | ||
CACNA1H | ENST00000565831.6 | c.3931A>G | p.Ile1311Val | missense_variant | 18/33 | 1 | ENSP00000455840.1 | |||
CACNA1H | ENST00000638323.1 | c.3892A>G | p.Ile1298Val | missense_variant | 19/35 | 5 | ENSP00000492267.1 | |||
CACNA1H | ENST00000569107.5 | c.154A>G | p.Ile52Val | missense_variant | 2/17 | 1 | ENSP00000454990.2 | |||
CACNA1H | ENST00000564231.5 | c.154A>G | p.Ile52Val | missense_variant | 2/18 | 1 | ENSP00000457555.2 | |||
CACNA1H | ENST00000562079.5 | c.154A>G | p.Ile52Val | missense_variant | 2/17 | 1 | ENSP00000454581.2 | |||
CACNA1H | ENST00000637236.2 | n.294A>G | non_coding_transcript_exon_variant | 3/6 | 5 | ENSP00000492650.2 | ||||
CACNA1H | ENST00000639478.1 | n.3931A>G | non_coding_transcript_exon_variant | 19/35 | 5 | ENSP00000491945.1 | ||||
CACNA1H | ENST00000640028.1 | n.*1844A>G | non_coding_transcript_exon_variant | 19/35 | 5 | ENSP00000491488.1 | ||||
CACNA1H | ENST00000640028.1 | n.*1844A>G | 3_prime_UTR_variant | 19/35 | 5 | ENSP00000491488.1 |
Frequencies
GnomAD3 genomes AF: 0.0000531 AC: 8AN: 150758Hom.: 0 Cov.: 27
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GnomAD3 exomes AF: 0.0000243 AC: 6AN: 247382Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134778
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GnomAD4 exome AF: 0.00000753 AC: 11AN: 1459980Hom.: 0 Cov.: 38 AF XY: 0.00000826 AC XY: 6AN XY: 726314
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GnomAD4 genome AF: 0.0000531 AC: 8AN: 150758Hom.: 0 Cov.: 27 AF XY: 0.0000544 AC XY: 4AN XY: 73490
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Idiopathic generalized epilepsy;C4310756:Hyperaldosteronism, familial, type IV Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 12, 2024 | This sequence change replaces isoleucine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 1311 of the CACNA1H protein (p.Ile1311Val). This variant is present in population databases (rs754671059, gnomAD 0.009%). 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: 460100). 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on 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:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Uncertain
CADD
Benign
DANN
Uncertain
DEOGEN2
Uncertain
D;.;.;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D;.
M_CAP
Uncertain
D
MetaRNN
Uncertain
T;T;T;T
MetaSVM
Pathogenic
D
MutationAssessor
Uncertain
M;.;M;M
PrimateAI
Uncertain
T
PROVEAN
Benign
N;.;N;N
REVEL
Uncertain
Sift
Benign
T;.;T;T
Sift4G
Benign
T;.;T;T
Polyphen
B;.;B;B
Vest4
MutPred
Gain of sheet (P = 0.0827);.;Gain of sheet (P = 0.0827);Gain of sheet (P = 0.0827);
MVP
ClinPred
D
GERP RS
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at