rs34658212

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_002252.5(KCNS3):​c.1145C>A​(p.Ala382Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000124 in 1,613,804 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 6.8e-7 ( 0 hom. )

Consequence

KCNS3
NM_002252.5 missense

Scores

12
7

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.665
Variant links:
Genes affected
KCNS3 (HGNC:6302): (potassium voltage-gated channel modifier subfamily S member 3) Voltage-gated potassium channels form the largest and most diversified class of ion channels and are present in both excitable and nonexcitable cells. Their main functions are associated with the regulation of the resting membrane potential and the control of the shape and frequency of action potentials. The alpha subunits are of 2 types: those that are functional by themselves and those that are electrically silent but capable of modulating the activity of specific functional alpha subunits. The protein encoded by this gene is not functional by itself but can form heteromultimers with member 1 and with member 2 (and possibly other members) of the Shab-related subfamily of potassium voltage-gated channel proteins. This gene belongs to the S subfamily of the potassium channel family. Alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Sep 2013]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
KCNS3NM_002252.5 linkc.1145C>A p.Ala382Glu missense_variant Exon 3 of 3 ENST00000304101.9 NP_002243.3 Q9BQ31
KCNS3NM_001282428.2 linkc.1145C>A p.Ala382Glu missense_variant Exon 3 of 3 NP_001269357.1 Q9BQ31
KCNS3XM_011532825.2 linkc.1145C>A p.Ala382Glu missense_variant Exon 4 of 4 XP_011531127.1 Q9BQ31
KCNS3XM_047444255.1 linkc.1145C>A p.Ala382Glu missense_variant Exon 3 of 3 XP_047300211.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
KCNS3ENST00000304101.9 linkc.1145C>A p.Ala382Glu missense_variant Exon 3 of 3 1 NM_002252.5 ENSP00000305824.4 Q9BQ31
KCNS3ENST00000403915.5 linkc.1145C>A p.Ala382Glu missense_variant Exon 3 of 3 1 ENSP00000385968.1 Q9BQ31
KCNS3ENST00000465292.5 linkn.305+14282C>A intron_variant Intron 2 of 4 4

Frequencies

GnomAD3 genomes
AF:
0.00000658
AC:
1
AN:
151958
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.00
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.000479
GnomAD3 exomes
AF:
0.00000398
AC:
1
AN:
251224
Hom.:
0
AF XY:
0.00000737
AC XY:
1
AN XY:
135762
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:
0.00000881
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
6.84e-7
AC:
1
AN:
1461846
Hom.:
0
Cov.:
41
AF XY:
0.00000138
AC XY:
1
AN XY:
727218
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:
0.00
Gnomad4 OTH exome
AF:
0.0000166
GnomAD4 genome
AF:
0.00000658
AC:
1
AN:
151958
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
74216
show subpopulations
Gnomad4 AFR
AF:
0.00
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.000479
Bravo
AF:
0.00000378
ExAC
AF:
0.00000824
AC:
1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.50
BayesDel_addAF
Uncertain
0.14
D
BayesDel_noAF
Uncertain
-0.030
CADD
Benign
13
DANN
Benign
0.86
DEOGEN2
Uncertain
0.65
D;D
Eigen
Benign
-0.70
Eigen_PC
Benign
-0.75
FATHMM_MKL
Benign
0.18
N
LIST_S2
Uncertain
0.94
.;D
M_CAP
Uncertain
0.28
D
MetaRNN
Uncertain
0.62
D;D
MetaSVM
Uncertain
0.74
D
MutationAssessor
Uncertain
2.4
M;M
PrimateAI
Benign
0.34
T
PROVEAN
Uncertain
-2.9
D;D
REVEL
Uncertain
0.48
Sift
Uncertain
0.025
D;D
Sift4G
Benign
0.073
T;T
Polyphen
0.17
B;B
Vest4
0.45
MutPred
0.69
Loss of ubiquitination at K384 (P = 0.0573);Loss of ubiquitination at K384 (P = 0.0573);
MVP
0.95
MPC
0.71
ClinPred
0.30
T
GERP RS
-0.094
Varity_R
0.23
gMVP
0.92

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: rs34658212; hg19: chr2-18113420; API