2-154698683-T-TCCC

Variant summary

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

The ENST00000544049.2(KCNJ3):c.-90_-88dup variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.00020 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0017 (1 hom.)
  • Failed GnomAD Quality Control
• Consequence: KCNJ3 ENST00000544049.2 5_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.896

Genes affected

KCNJ3 (HGNC:6264): (potassium inwardly rectifying channel subfamily J member 3) 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, is controlled by G-proteins and plays an important role in regulating heartbeat. It associates with three other G-protein-activated potassium channels to form a heteromultimeric pore-forming complex that also couples to neurotransmitter receptors in the brain and whereby channel activation can inhibit action potential firing by hyperpolarizing the plasma membrane. These multimeric G-protein-gated inwardly-rectifying potassium (GIRK) channels may play a role in the pathophysiology of epilepsy, addiction, Down's syndrome, ataxia, and Parkinson's disease. Alternative splicing results in multiple transcript variants encoding distinct proteins. [provided by RefSeq, May 2012]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KCNJ3	NM_002239.4			upstream_gene_variant		ENST00000295101.3
KCNJ3	NM_001260508.2			upstream_gene_variant
KCNJ3	NM_001260509.2			upstream_gene_variant
KCNJ3	NM_001260510.2			upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KCNJ3	ENST00000544049.2	c.-90_-88dup		5_prime_UTR_variant	1/2	1
KCNJ3	ENST00000651198.1	c.-42-585_-42-583dup		intron_variant
KCNJ3	ENST00000295101.3			upstream_gene_variant		1	NM_002239.4	P1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 23 AN: 114400 Hom.: 0 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.000453

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000891

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000368

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000128

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000122

Gnomad OTH AF: 0.000635

GnomAD4 exome AF: 0.00168 AC: 121 AN: 71944 Hom.: 1 Cov.: 2 AF XY: 0.00163 AC XY: 64 AN XY: 39224

Gnomad4 AFR exome AF: 0.00223

Gnomad4 AMR exome AF: 0.00331

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00225

Gnomad4 SAS exome AF: 0.00270

Gnomad4 FIN exome AF: 0.000272

Gnomad4 NFE exome AF: 0.00157

Gnomad4 OTH exome AF: 0.00371

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.000201 AC: 23 AN: 114400 Hom.: 0 Cov.: 0 AF XY: 0.000200 AC XY: 11 AN XY: 55002

Gnomad4 AFR AF: 0.000453

Gnomad4 AMR AF: 0.0000891

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000368

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000128

Gnomad4 NFE AF: 0.000122

Gnomad4 OTH AF: 0.000635

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs5835535; hg19: chr2-155555195;