GeneBe

17-70175238-CGG-AGA

Variant names:
GermlineCancer (beta)

Variant summary

Our verdict is Uncertain significance.
+1 Uncertain · Cold
-7
-6
-1
0
+5
+6
+9
+10
B
LB
VUS
LP
P
 The variant received 1 classification points (ACGS-UK Somatic Oncogenicity v2025). O3_ModerateB4_Supporting

The NM_000891.3(KCNJ2):c.199_201delCGGinsAGA (p.68) variant causes a synonymous change. The gene KCNJ2 is a known oncogene (CancerMine: 2 oncogene, 1 driver citations). The gene KCNJ2 is a cancer driver gene (CancerMine: 2 oncogene, 1 driver citations). Note: allele frequency estimates from gnomAD may be inaccurate for this variant type (MNP or indel longer than 3 bp) due to technology limitations. The variant is absent from the gnomAD population database at sites with sufficient sequencing coverage. The affected nucleotide is highly conserved across species (PhyloP 100-way vertebrate score: 10.00). No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)

Consequence

KCNJ2
NM_000891.3 synonymous

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 10.0

Publications

0 publications found
Variant links:
Genes affected
KCNJ2 (HGNC:6263): (potassium inwardly rectifying channel subfamily J member 2) Potassium channels are present in most mammalian cells, where they participate in a wide range of physiologic responses. The protein encoded by this gene is an integral membrane protein and inward-rectifier type potassium channel. The encoded protein, which has a greater tendency to allow potassium to flow into a cell rather than out of a cell, probably participates in establishing action potential waveform and excitability of neuronal and muscle tissues. Mutations in this gene have been associated with Andersen syndrome, which is characterized by periodic paralysis, cardiac arrhythmias, and dysmorphic features. [provided by RefSeq, Jul 2008]
KCNJ2 Gene-Disease associations (from GenCC):
  • Andersen-Tawil syndrome
    Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, PanelApp Australia, Orphanet, Labcorp Genetics (formerly Invitae), Genomics England PanelApp
  • atrial fibrillation, familial, 9
    Inheritance: AD Classification: STRONG Submitted by: PanelApp Australia
  • short QT syndrome type 3
    Inheritance: AD Classification: STRONG, MODERATE Submitted by: PanelApp Australia, G2P, Labcorp Genetics (formerly Invitae)
  • short QT syndrome
    Inheritance: AD Classification: MODERATE, SUPPORTIVE Submitted by: ClinGen, Orphanet
  • familial atrial fibrillation
    Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
  • catecholaminergic polymorphic ventricular tachycardia
    Inheritance: AD Classification: LIMITED, NO_KNOWN Submitted by: Genomics England PanelApp, ClinGen, G2P
  • long QT syndrome
    Inheritance: AD Classification: LIMITED Submitted by: ClinGen, G2P
  • congenital heart disease
    Inheritance: Unknown Classification: NO_KNOWN Submitted by: ClinGen

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_000891.3, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

Classification according to ACGS-UK Somatic Oncogenicity v2025

Classification was made for transcript:

Our verdict: Uncertain_significance. The variant received 1 points.

O3Absent or very rare in population
Absent or extremely rare in gnomAD (AC ≤ 2) — O3 moderate; GnomAD: AF = absent, AC = 0 — absent/extremely rare (O3 moderate [+2])
B4Synonymous/intronic, no splicing impact
Synonymous/intronic variant outside canonical splice sites (B4 supporting); Synonymous variant — splicing impact not confirmed absent; B4 supporting [-1]

Variant Effect in Transcripts

Automated classification analysis was done for transcript: NM_000891.3. You can select a different transcript below to see updated classification assignments.

RefSeq Transcripts

KCNJ2 NM_000891.3
MANE Select
HGVSc / HGVSpc.199_201delCGGinsAGAp.68
Exon rankN/A
synonymous
Prot: NP_000882.1UniProt: P63252

Ensembl Transcripts

KCNJ2 ENST00000243457.4
TSL:1MANE Select
HGVSc / HGVSpc.199_201delCGGinsAGAp.68
Exon rankN/A
synonymous
Prot: ENSP00000243457.2UniProt: P63252
KCNJ2 ENST00000535240.1
TSL:1
HGVSc / HGVSpc.199_201delCGGinsAGAp.68
Exon rankN/A
synonymous
Prot: ENSP00000441848.1UniProt: P63252
KCNJ2 ENST00000854891.1
HGVSc / HGVSpc.199_201delCGGinsAGAp.68
Exon rankN/A
synonymous
Prot: ENSP00000524950.1UniProt: P63252

Frequencies

Allele frequencies (AF), counts (AC/AN), homozygotes and coverage

Common (AF > 0.05 / Hom > 5)
Rare (AF ≤ 0.0001 / Hom ≤ 1)
Global population databases 2 sources
GnomAD3 genomes
Cov:32
GnomAD4 genome
Cov:32
Showing 2 sources

ClinVar

Not reported in ClinVar

Computational Scores

PhyloP100
Pathogenic10
Showing 1 of 1 scores

Splicing Scores

No splicing scores have been computed for this variant.

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

MaveDB functional evidence

MaveDB is a public repository of laboratory assays that test the effect of thousands of variants at once — treat this as supporting research data and interpret it with great caution; it is not a clinical classification.

No MaveDB functional evidence found for this variant.

Publications

Other links and lift over

hg19: chr17-68171379;
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