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GeneBe

rs1805127

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate

The NM_000219.6(KCNE1):c.112A>C(p.Ser38Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict 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. S38D) has been classified as Likely benign.

Frequency

Genomes: not found (cov: 12)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

KCNE1
NM_000219.6 missense

Scores

3
15

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.04
Variant links:
Genes affected
KCNE1 (HGNC:6240): (potassium voltage-gated channel subfamily E regulatory subunit 1) The product of this gene belongs to the potassium channel KCNE family. Potassium ion channels are essential to many cellular functions and show a high degree of diversity, varying in their electrophysiologic and pharmacologic properties. This gene encodes a transmembrane protein known to associate with the product of the KVLQT1 gene to form the delayed rectifier potassium channel. Mutation in this gene are associated with both Jervell and Lange-Nielsen and Romano-Ward forms of long-QT syndrome. Alternatively spliced transcript variants encoding the same protein have been identified. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

BP4
Computational evidence support a benign effect (MetaRNN=0.10619265).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
KCNE1NM_000219.6 linkuse as main transcriptc.112A>C p.Ser38Arg missense_variant 4/4 ENST00000399286.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
KCNE1ENST00000399286.3 linkuse as main transcriptc.112A>C p.Ser38Arg missense_variant 4/41 NM_000219.6 P1

Frequencies

GnomAD3 genomes
Cov.:
12
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
0.00
AC:
0
AN:
844044
Hom.:
0
Cov.:
23
AF XY:
0.00
AC XY:
0
AN XY:
419742
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:
0.00
GnomAD4 genome
Cov.:
12

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.12
BayesDel_addAF
Benign
-0.0042
T
BayesDel_noAF
Benign
-0.24
Cadd
Benign
7.2
Dann
Benign
0.93
DEOGEN2
Uncertain
0.56
D;D;D;D;D;D;D;D
Eigen
Benign
-1.4
Eigen_PC
Benign
-1.4
FATHMM_MKL
Benign
0.066
N
M_CAP
Uncertain
0.17
D
MetaRNN
Benign
0.11
T;T;T;T;T;T;T;T
MetaSVM
Benign
-0.48
T
MutationAssessor
Benign
0.34
N;N;N;N;N;N;N;N
MutationTaster
Benign
1.0
N;N;N;N;N;N
PrimateAI
Benign
0.31
T
PROVEAN
Benign
-1.3
N;.;.;N;N;N;N;N
REVEL
Uncertain
0.32
Sift
Benign
0.24
T;.;.;T;T;T;T;T
Sift4G
Benign
0.51
T;T;T;T;T;T;T;T
Polyphen
0.0030
B;B;B;B;B;B;B;B
Vest4
0.058
MutPred
0.20
Gain of solvent accessibility (P = 0.0155);Gain of solvent accessibility (P = 0.0155);Gain of solvent accessibility (P = 0.0155);Gain of solvent accessibility (P = 0.0155);Gain of solvent accessibility (P = 0.0155);Gain of solvent accessibility (P = 0.0155);Gain of solvent accessibility (P = 0.0155);Gain of solvent accessibility (P = 0.0155);
MVP
0.57
MPC
0.093
ClinPred
0.039
T
GERP RS
0.18
Varity_R
0.071
gMVP
0.46

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: rs1805127; hg19: chr21-35821821; API