GeneBe

1-181483210-G-A

Variant names:

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000367570.6(CACNA1E):​c.-535G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

CACNA1E
ENST00000367570.6 5_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.13

Publications

0 publications found
Variant links:
Genes affected
CACNA1E (HGNC:1392): (calcium voltage-gated channel subunit alpha1 E) Voltage-dependent calcium channels are multisubunit complexes consisting of alpha-1, alpha-2, beta, and delta subunits in a 1:1:1:1 ratio. These channels mediate the entry of calcium ions into excitable cells, and are also involved in a variety of calcium-dependent processes, including muscle contraction, hormone or neurotransmitter release, gene expression, cell motility, cell division and cell death. This gene encodes the alpha-1E subunit of the R-type calcium channels, which belong to the 'high-voltage activated' group that maybe involved in the modulation of firing patterns of neurons important for information processing. Alternatively spliced transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Apr 2011]
CACNA1E Gene-Disease associations (from GenCC):
  • developmental and epileptic encephalopathy, 69
    Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae), G2P, Illumina
  • genetic developmental and epileptic encephalopathy
    Inheritance: AD Classification: DEFINITIVE Submitted by: ClinGen
  • neurodevelopmental disorder
    Inheritance: AD Classification: MODERATE Submitted by: Ambry Genetics

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CACNA1EXM_017002243.2 linkc.435-534G>A intron_variant Intron 2 of 49 XP_016857732.1
CACNA1EXM_017002244.2 linkc.435-534G>A intron_variant Intron 2 of 49 XP_016857733.1
CACNA1EXM_017002251.1 linkc.435-534G>A intron_variant Intron 2 of 49 XP_016857740.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CACNA1EENST00000367570.6 linkc.-535G>A 5_prime_UTR_variant Exon 1 of 47 1 ENSP00000356542.1 Q15878-3
CACNA1EENST00000524607.6 linkc.435-534G>A intron_variant Intron 2 of 11 5 ENSP00000432038.2 E9PIE8
CACNA1EENST00000533229.1 linkn.-101G>A upstream_gene_variant 1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
72
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
40
African (AFR)
AF:
0.00
AC:
0
AN:
8
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
4
East Asian (EAS)
AF:
0.00
AC:
0
AN:
2
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
8
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
44
Other (OTH)
AF:
0.00
AC:
0
AN:
6
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.77
CADD
Benign
0.62
DANN
Benign
0.91
PhyloP100
-1.1
PromoterAI
-0.053
Neutral

Splicing

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

Publications

Other links and lift over

dbSNP: rs182525961; hg19: chr1-181452346; API