rs118192186
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PVS1PM2
The NM_172107.4(KCNQ2):āc.2T>Gā(p.Met1?) variant causes a start lost change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: š 0.0 ( 0 hom., cov: 31)
Failed GnomAD Quality Control
Consequence
KCNQ2
NM_172107.4 start_lost
NM_172107.4 start_lost
Scores
8
1
7
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 2.59
Genes affected
KCNQ2 (HGNC:6296): (potassium voltage-gated channel subfamily Q member 2) The M channel is a slowly activating and deactivating potassium channel that plays a critical role in the regulation of neuronal excitability. The M channel is formed by the association of the protein encoded by this gene and a related protein encoded by the KCNQ3 gene, both integral membrane proteins. M channel currents are inhibited by M1 muscarinic acetylcholine receptors and activated by retigabine, a novel anti-convulsant drug. Defects in this gene are a cause of benign familial neonatal convulsions type 1 (BFNC), also known as epilepsy, benign neonatal type 1 (EBN1). At least five transcript variants encoding five different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 10 ACMG points.
PVS1
Start lost variant, next in-frame start position is after 10 pathogenic variants. Next in-frame start position is after 174 codons. Genomic position: 63444829. Lost 0.199 part of the original CDS.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes 0.00 AC: 0AN: 150862Hom.: 0 Cov.: 31 FAILED QC
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GnomAD4 exome Cov.: 32
GnomAD4 exome
Cov.:
32
GnomAD4 genome 0.00 AC: 0AN: 150862Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 73642
GnomAD4 genome
Data not reliable, filtered out with message: AC0;AS_VQSR
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150862
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31
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73642
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ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Uncertain
DANN
Benign
DEOGEN2
Benign
.;.;T;T;T;T;.;.;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
D
LIST_S2
Uncertain
D;D;D;D;D;D;D;D;D
M_CAP
Pathogenic
D
MetaRNN
Pathogenic
D;D;D;D;D;D;D;D;D
MetaSVM
Pathogenic
D
PROVEAN
Benign
.;.;.;.;N;N;N;N;N
REVEL
Pathogenic
Sift
Pathogenic
.;.;.;.;D;D;D;D;D
Sift4G
Pathogenic
D;D;D;D;D;D;D;D;D
Polyphen
D;.;.;.;.;D;D;D;.
Vest4
MutPred
Gain of MoRF binding (P = 0.0391);Gain of MoRF binding (P = 0.0391);Gain of MoRF binding (P = 0.0391);Gain of MoRF binding (P = 0.0391);Gain of MoRF binding (P = 0.0391);Gain of MoRF binding (P = 0.0391);Gain of MoRF binding (P = 0.0391);Gain of MoRF binding (P = 0.0391);Gain of MoRF binding (P = 0.0391);
MVP
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.