rs1361083258
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM1PM2PM5PP2PP3_Strong
The NM_001205293.3(CACNA1E):c.2069G>A(p.Gly690Asp) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging 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. G690V) has been classified as Likely pathogenic.
Frequency
Consequence
NM_001205293.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CACNA1E | NM_001205293.3 | c.2069G>A | p.Gly690Asp | missense_variant | 16/48 | ENST00000367573.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CACNA1E | ENST00000367573.7 | c.2069G>A | p.Gly690Asp | missense_variant | 16/48 | 1 | NM_001205293.3 | A2 | |
CACNA1E | ENST00000367570.6 | c.2069G>A | p.Gly690Asp | missense_variant | 16/47 | 1 | P4 | ||
CACNA1E | ENST00000621791.4 | c.2069G>A | p.Gly690Asp | missense_variant | 16/46 | 1 | A2 | ||
CACNA1E | ENST00000360108.7 | c.2069G>A | p.Gly690Asp | missense_variant | 16/47 | 5 | A2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 27
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Early infantile epileptic encephalopathy with suppression bursts Pathogenic:1
Likely pathogenic, no assertion criteria provided | literature only | Yale Center for Mendelian Genomics, Yale University | Nov 01, 2018 | - - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 05, 2016 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at