rs201253748

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_000718.4(CACNA1B):​c.92G>A​(p.Gly31Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000894 in 1,118,592 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G31V) has been classified as Benign.

Frequency

Genomes: not found (cov: 34)
Exomes 𝑓: 8.9e-7 ( 0 hom. )

Consequence

CACNA1B
NM_000718.4 missense

Scores

2
8
9

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.854
Variant links:
Genes affected
CACNA1B (HGNC:1389): (calcium voltage-gated channel subunit alpha1 B) The protein encoded by this gene is the pore-forming subunit of an N-type voltage-dependent calcium channel, which controls neurotransmitter release from neurons. The encoded protein forms a complex with alpha-2, beta, and delta subunits to form the high-voltage activated channel. This channel is sensitive to omega-conotoxin-GVIA and omega-agatoxin-IIIA but insensitive to dihydropyridines. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2011]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.34517425).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CACNA1BNM_000718.4 linkc.92G>A p.Gly31Asp missense_variant Exon 1 of 47 ENST00000371372.6 NP_000709.1 Q00975-1
CACNA1BNM_001243812.2 linkc.92G>A p.Gly31Asp missense_variant Exon 1 of 47 NP_001230741.1 Q00975-2
LOC100133077NR_121583.1 linkn.2692-2345C>T intron_variant Intron 2 of 3

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CACNA1BENST00000371372.6 linkc.92G>A p.Gly31Asp missense_variant Exon 1 of 47 5 NM_000718.4 ENSP00000360423.1 Q00975-1
CACNA1BENST00000371357.5 linkc.92G>A p.Gly31Asp missense_variant Exon 1 of 46 5 ENSP00000360408.1 B1AQK7
CACNA1BENST00000371363.5 linkc.92G>A p.Gly31Asp missense_variant Exon 1 of 46 5 ENSP00000360414.1 B1AQK6
CACNA1BENST00000277551.6 linkc.92G>A p.Gly31Asp missense_variant Exon 1 of 47 5 ENSP00000277551.2 Q00975-2

Frequencies

GnomAD3 genomes
Cov.:
34
GnomAD3 exomes
AF:
0.0000163
AC:
1
AN:
61328
Hom.:
0
AF XY:
0.0000285
AC XY:
1
AN XY:
35120
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000452
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
8.94e-7
AC:
1
AN:
1118592
Hom.:
0
Cov.:
32
AF XY:
0.00000185
AC XY:
1
AN XY:
539564
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000107
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.53
BayesDel_addAF
Uncertain
0.12
D
BayesDel_noAF
Uncertain
-0.070
CADD
Uncertain
24
DANN
Uncertain
1.0
DEOGEN2
Benign
0.29
.;.;T;T;.;T
Eigen
Benign
-0.51
Eigen_PC
Benign
-0.45
FATHMM_MKL
Benign
0.46
N
LIST_S2
Benign
0.59
T;T;T;T;T;T
M_CAP
Pathogenic
0.99
D
MetaRNN
Benign
0.35
T;T;T;T;T;T
MetaSVM
Uncertain
0.037
D
MutationAssessor
Benign
1.4
L;.;L;.;.;.
PrimateAI
Pathogenic
0.92
D
PROVEAN
Benign
-1.7
N;.;N;N;N;N
REVEL
Uncertain
0.39
Sift
Uncertain
0.019
D;.;T;T;T;T
Sift4G
Uncertain
0.0030
D;D;D;D;D;D
Polyphen
0.0010
.;.;.;B;.;.
Vest4
0.28
MutPred
0.26
Loss of glycosylation at P32 (P = 0.07);Loss of glycosylation at P32 (P = 0.07);Loss of glycosylation at P32 (P = 0.07);Loss of glycosylation at P32 (P = 0.07);Loss of glycosylation at P32 (P = 0.07);Loss of glycosylation at P32 (P = 0.07);
MVP
0.80
MPC
1.4
ClinPred
0.22
T
GERP RS
1.3
Varity_R
0.15
gMVP
0.43

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs201253748; hg19: chr9-140772477; API