rs34658212
Variant names:
Your query was ambiguous. Multiple possible variants found:
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
NM_002252.5 missense
Scores
12
7
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.665
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]
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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 |
---|---|---|---|---|---|---|---|---|
KCNS3 | NM_002252.5 | c.1145C>A | p.Ala382Glu | missense_variant | Exon 3 of 3 | ENST00000304101.9 | NP_002243.3 | |
KCNS3 | NM_001282428.2 | c.1145C>A | p.Ala382Glu | missense_variant | Exon 3 of 3 | NP_001269357.1 | ||
KCNS3 | XM_011532825.2 | c.1145C>A | p.Ala382Glu | missense_variant | Exon 4 of 4 | XP_011531127.1 | ||
KCNS3 | XM_047444255.1 | c.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 |
---|---|---|---|---|---|---|---|---|---|---|
KCNS3 | ENST00000304101.9 | c.1145C>A | p.Ala382Glu | missense_variant | Exon 3 of 3 | 1 | NM_002252.5 | ENSP00000305824.4 | ||
KCNS3 | ENST00000403915.5 | c.1145C>A | p.Ala382Glu | missense_variant | Exon 3 of 3 | 1 | ENSP00000385968.1 | |||
KCNS3 | ENST00000465292.5 | n.305+14282C>A | intron_variant | Intron 2 of 4 | 4 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151958Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251224Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135762
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GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461846Hom.: 0 Cov.: 41 AF XY: 0.00000138 AC XY: 1AN XY: 727218
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GnomAD4 genome AF: 0.00000658 AC: 1AN: 151958Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74216
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Uncertain
CADD
Benign
DANN
Benign
DEOGEN2
Uncertain
D;D
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Uncertain
.;D
M_CAP
Uncertain
D
MetaRNN
Uncertain
D;D
MetaSVM
Uncertain
D
MutationAssessor
Uncertain
M;M
PrimateAI
Benign
T
PROVEAN
Uncertain
D;D
REVEL
Uncertain
Sift
Uncertain
D;D
Sift4G
Benign
T;T
Polyphen
B;B
Vest4
MutPred
Loss of ubiquitination at K384 (P = 0.0573);Loss of ubiquitination at K384 (P = 0.0573);
MVP
MPC
ClinPred
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gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at