GeneBe

NM_021098.3:c.-509_-476delCGCGTCTCGGGCCGGGGGCGGATCCTCCCCAGTA

Variant names:

Variant summary

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

The NM_021098.3(CACNA1H):​c.-509_-476delCGCGTCTCGGGCCGGGGGCGGATCCTCCCCAGTA variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 26)

Consequence

CACNA1H
NM_021098.3 upstream_gene

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.21

Publications

0 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)

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ACMG classification

Classification was made for transcript

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

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CACNA1HNM_021098.3 linkc.-509_-476delCGCGTCTCGGGCCGGGGGCGGATCCTCCCCAGTA upstream_gene_variant ENST00000348261.11 NP_066921.2 O95180-1B3KQH9

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CACNA1HENST00000348261.11 linkc.-509_-476delCGCGTCTCGGGCCGGGGGCGGATCCTCCCCAGTA upstream_gene_variant 1 NM_021098.3 ENSP00000334198.7 O95180-1
CACNA1HENST00000569107.6 linkc.-509_-476delCGCGTCTCGGGCCGGGGGCGGATCCTCCCCAGTA upstream_gene_variant 1 ENSP00000454990.2 H3BNT0
CACNA1HENST00000711493.1 linkc.-509_-476delCGCGTCTCGGGCCGGGGGCGGATCCTCCCCAGTA upstream_gene_variant ENSP00000518778.1
CACNA1HENST00000565831.7 linkc.-509_-476delCGCGTCTCGGGCCGGGGGCGGATCCTCCCCAGTA upstream_gene_variant 1 ENSP00000455840.1 O95180-2
CACNA1HENST00000711450.1 linkc.-509_-476delCGCGTCTCGGGCCGGGGGCGGATCCTCCCCAGTA upstream_gene_variant ENSP00000518762.1
CACNA1HENST00000564231.6 linkc.-509_-476delCGCGTCTCGGGCCGGGGGCGGATCCTCCCCAGTA upstream_gene_variant 1 ENSP00000457555.2 H3BUA8
CACNA1HENST00000638323.1 linkc.-509_-476delCGCGTCTCGGGCCGGGGGCGGATCCTCCCCAGTA upstream_gene_variant 5 ENSP00000492267.1 A0A1W2PR14
CACNA1HENST00000562079.6 linkc.-509_-476delCGCGTCTCGGGCCGGGGGCGGATCCTCCCCAGTA upstream_gene_variant 1 ENSP00000454581.2 H3BMW6
CACNA1HENST00000711482.1 linkc.-509_-476delCGCGTCTCGGGCCGGGGGCGGATCCTCCCCAGTA upstream_gene_variant ENSP00000518771.1
CACNA1HENST00000711485.1 linkc.-509_-476delCGCGTCTCGGGCCGGGGGCGGATCCTCCCCAGTA upstream_gene_variant ENSP00000518774.1
CACNA1HENST00000711455.1 linkc.-509_-476delCGCGTCTCGGGCCGGGGGCGGATCCTCCCCAGTA upstream_gene_variant ENSP00000518768.1
CACNA1HENST00000711483.1 linkc.-509_-476delCGCGTCTCGGGCCGGGGGCGGATCCTCCCCAGTA upstream_gene_variant ENSP00000518772.1
CACNA1HENST00000711456.1 linkc.-509_-476delCGCGTCTCGGGCCGGGGGCGGATCCTCCCCAGTA upstream_gene_variant ENSP00000518769.1
CACNA1HENST00000621827.2 linkn.-509_-476delCGCGTCTCGGGCCGGGGGCGGATCCTCCCCAGTA upstream_gene_variant 6 ENSP00000518766.1
CACNA1HENST00000637236.3 linkn.-509_-476delCGCGTCTCGGGCCGGGGGCGGATCCTCCCCAGTA upstream_gene_variant 5 ENSP00000492650.2 A0A1W2PS38
CACNA1HENST00000639478.1 linkn.-509_-476delCGCGTCTCGGGCCGGGGGCGGATCCTCCCCAGTA upstream_gene_variant 5 ENSP00000491945.1 A0A1W2PQW2
CACNA1HENST00000640028.1 linkn.-509_-476delCGCGTCTCGGGCCGGGGGCGGATCCTCCCCAGTA upstream_gene_variant 5 ENSP00000491488.1 A0A1W2PQ19
CACNA1HENST00000711442.1 linkn.-509_-476delCGCGTCTCGGGCCGGGGGCGGATCCTCCCCAGTA upstream_gene_variant ENSP00000518758.1
CACNA1HENST00000711448.1 linkn.-509_-476delCGCGTCTCGGGCCGGGGGCGGATCCTCCCCAGTA upstream_gene_variant ENSP00000518760.1
CACNA1HENST00000711449.1 linkn.-509_-476delCGCGTCTCGGGCCGGGGGCGGATCCTCCCCAGTA upstream_gene_variant ENSP00000518761.1
CACNA1HENST00000711451.1 linkn.-509_-476delCGCGTCTCGGGCCGGGGGCGGATCCTCCCCAGTA upstream_gene_variant ENSP00000518763.1
CACNA1HENST00000711452.1 linkn.-509_-476delCGCGTCTCGGGCCGGGGGCGGATCCTCCCCAGTA upstream_gene_variant ENSP00000518764.1
CACNA1HENST00000711453.1 linkn.-509_-476delCGCGTCTCGGGCCGGGGGCGGATCCTCCCCAGTA upstream_gene_variant ENSP00000518765.1
CACNA1HENST00000711484.1 linkn.-509_-476delCGCGTCTCGGGCCGGGGGCGGATCCTCCCCAGTA upstream_gene_variant ENSP00000518773.1
CACNA1HENST00000711486.1 linkn.-509_-476delCGCGTCTCGGGCCGGGGGCGGATCCTCCCCAGTA upstream_gene_variant ENSP00000518775.1
CACNA1HENST00000711487.1 linkn.-509_-476delCGCGTCTCGGGCCGGGGGCGGATCCTCCCCAGTA upstream_gene_variant ENSP00000518776.1
CACNA1HENST00000711488.1 linkn.-509_-476delCGCGTCTCGGGCCGGGGGCGGATCCTCCCCAGTA upstream_gene_variant ENSP00000518777.1

Frequencies

GnomAD3 genomes
Cov.:
26
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
26

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
PhyloP100
1.2

Splicing

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

Publications

Other links and lift over

hg19: chr16-1202979; API