rs886037945
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM1PM2PM5PP2PP3_ModeratePP5
The NM_001127222.2(CACNA1A):c.2134G>T(p.Ala712Ser) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. A712T) has been classified as Pathogenic.
Frequency
Consequence
NM_001127222.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CACNA1A | ENST00000360228.11 | c.2134G>T | p.Ala712Ser | missense_variant | Exon 17 of 47 | 1 | NM_001127222.2 | ENSP00000353362.5 | ||
CACNA1A | ENST00000638029.1 | c.2137G>T | p.Ala713Ser | missense_variant | Exon 17 of 48 | 5 | ENSP00000489829.1 | |||
CACNA1A | ENST00000573710.7 | c.2140G>T | p.Ala714Ser | missense_variant | Exon 17 of 47 | 5 | ENSP00000460092.3 | |||
CACNA1A | ENST00000635727.1 | c.2137G>T | p.Ala713Ser | missense_variant | Exon 17 of 47 | 5 | ENSP00000490001.1 | |||
CACNA1A | ENST00000637769.1 | c.2137G>T | p.Ala713Ser | missense_variant | Exon 17 of 47 | 1 | ENSP00000489778.1 | |||
CACNA1A | ENST00000636012.1 | c.2137G>T | p.Ala713Ser | missense_variant | Exon 17 of 46 | 5 | ENSP00000490223.1 | |||
CACNA1A | ENST00000637736.1 | c.1996G>T | p.Ala666Ser | missense_variant | Exon 16 of 46 | 5 | ENSP00000489861.1 | |||
CACNA1A | ENST00000636389.1 | c.2137G>T | p.Ala713Ser | missense_variant | Exon 17 of 47 | 5 | ENSP00000489992.1 | |||
CACNA1A | ENST00000637432.1 | c.2137G>T | p.Ala713Ser | missense_variant | Exon 17 of 48 | 5 | ENSP00000490617.1 | |||
CACNA1A | ENST00000636549.1 | c.2137G>T | p.Ala713Ser | missense_variant | Exon 17 of 48 | 5 | ENSP00000490578.1 | |||
CACNA1A | ENST00000637927.1 | c.2140G>T | p.Ala714Ser | missense_variant | Exon 17 of 47 | 5 | ENSP00000489715.1 | |||
CACNA1A | ENST00000635895.1 | c.2137G>T | p.Ala713Ser | missense_variant | Exon 17 of 47 | 5 | ENSP00000490323.1 | |||
CACNA1A | ENST00000638009.2 | c.2137G>T | p.Ala713Ser | missense_variant | Exon 17 of 47 | 1 | ENSP00000489913.1 | |||
CACNA1A | ENST00000637276.1 | c.2137G>T | p.Ala713Ser | missense_variant | Exon 17 of 46 | 5 | ENSP00000489777.1 |
Frequencies
GnomAD3 genomes Cov.: 29
GnomAD4 exome Cov.: 32
GnomAD4 genome Cov.: 29
ClinVar
Submissions by phenotype
Developmental and epileptic encephalopathy, 42 Pathogenic:1
We consider the variant NM_001127221.2:c.2137G>T as disease-causing; it results in an amino acid substitution. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at