rs1057520918
Variant summary
Our verdict is Pathogenic. Variant got 13 ACMG points: 13P and 0B. PM1PM2PM5PP2PP3_StrongPP5_Moderate
The NM_001127222.2(CACNA1A):c.4043G>C(p.Arg1348Pro) 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 Likely pathogenic (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1348Q) has been classified as Likely pathogenic.
Frequency
Consequence
NM_001127222.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 13 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CACNA1A | ENST00000360228.11 | c.4043G>C | p.Arg1348Pro | missense_variant | 25/47 | 1 | NM_001127222.2 | ENSP00000353362.5 | ||
CACNA1A | ENST00000638029.1 | c.4055G>C | p.Arg1352Pro | missense_variant | 25/48 | 5 | ENSP00000489829.1 | |||
CACNA1A | ENST00000573710.7 | c.4049G>C | p.Arg1350Pro | missense_variant | 25/47 | 5 | ENSP00000460092.3 | |||
CACNA1A | ENST00000635727.1 | c.4046G>C | p.Arg1349Pro | missense_variant | 25/47 | 5 | ENSP00000490001.1 | |||
CACNA1A | ENST00000637769.1 | c.4046G>C | p.Arg1349Pro | missense_variant | 25/47 | 1 | ENSP00000489778.1 | |||
CACNA1A | ENST00000636012.1 | c.4046G>C | p.Arg1349Pro | missense_variant | 25/46 | 5 | ENSP00000490223.1 | |||
CACNA1A | ENST00000637736.1 | c.3905G>C | p.Arg1302Pro | missense_variant | 24/46 | 5 | ENSP00000489861.1 | |||
CACNA1A | ENST00000636389.1 | c.4046G>C | p.Arg1349Pro | missense_variant | 25/47 | 5 | ENSP00000489992.1 | |||
CACNA1A | ENST00000637432.1 | c.4055G>C | p.Arg1352Pro | missense_variant | 25/48 | 5 | ENSP00000490617.1 | |||
CACNA1A | ENST00000636549.1 | c.4046G>C | p.Arg1349Pro | missense_variant | 25/48 | 5 | ENSP00000490578.1 | |||
CACNA1A | ENST00000637927.1 | c.4049G>C | p.Arg1350Pro | missense_variant | 25/47 | 5 | ENSP00000489715.1 | |||
CACNA1A | ENST00000635895.1 | c.4046G>C | p.Arg1349Pro | missense_variant | 25/47 | 5 | ENSP00000490323.1 | |||
CACNA1A | ENST00000638009.2 | c.4046G>C | p.Arg1349Pro | missense_variant | 25/47 | 1 | ENSP00000489913.1 | |||
CACNA1A | ENST00000637276.1 | c.4046G>C | p.Arg1349Pro | missense_variant | 25/46 | 5 | ENSP00000489777.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 30
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Sep 26, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.