Genetic Variant KCNJ3:c.-89_-88dupCC (chr2-154698683-T-TCC) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BS2

The ENST00000544049.2(KCNJ3):c.-89_-88dupCC 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 0.0000087 ( 0 hom., cov: 0)

Exomes 𝑓: 0.0083 ( 134 hom. )

Consequence

KCNJ3
ENST00000544049.2 5_prime_UTR

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.896

Publications

0 publications found

Variant links:

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]

KCNJ3 links:

ENSG00000287900 (HGNC:):

ENSG00000287900 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BS2

High Homozygotes in GnomAdExome4 at 134 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000544049.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
KCNJ3	NM_002239.4	MANE Select	c.-93_-92insCC	upstream_gene	N/A	NP_002230.1	P48549-1
KCNJ3	NM_001260509.2		c.-93_-92insCC	upstream_gene	N/A	NP_001247438.1	D2X9V0
KCNJ3	NM_001260510.2		c.-93_-92insCC	upstream_gene	N/A	NP_001247439.1	D2XBF0

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
KCNJ3	ENST00000544049.2	TSL:1	c.-89_-88dupCC	5_prime_UTR	Exon 1 of 2	ENSP00000438410.1	P48549-2
KCNJ3	ENST00000651198.1		c.-42-584_-42-583dupCC	intron	N/A	ENSP00000498639.1	A0A494C0M7
ENSG00000287900	ENST00000803267.1		n.768_769dupGG	non_coding_transcript_exon	Exon 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.00000874

AC:

AN:

114452

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00382

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.00827

AC:

595

AN:

71946

Hom.:

134

Cov.:

AF XY:

0.00783

AC XY:

307

AN XY:

39226

show subpopulations

African (AFR)

AF:

0.00191

AC:

AN:

3144

American (AMR)

AF:

0.0113

AC:

AN:

5732

Ashkenazi Jewish (ASJ)

AF:

0.0185

AC:

AN:

812

East Asian (EAS)

AF:

0.000205

AC:

AN:

4884

South Asian (SAS)

AF:

0.0120

AC:

AN:

8164

European-Finnish (FIN)

AF:

0.00170

AC:

AN:

14704

Middle Eastern (MID)

AF:

0.00158

AC:

AN:

1268

European-Non Finnish (NFE)

AF:

0.0114

AC:

347

AN:

30544

Other (OTH)

AF:

0.0134

AC:

AN:

2694

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.751

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00000873

AC:

AN:

114504

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

55080

show subpopulations

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.00

AC:

AN:

26552

American (AMR)

AF:

0.00

AC:

AN:

11242

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2872

East Asian (EAS)

AF:

0.00

AC:

AN:

2710

South Asian (SAS)

AF:

0.00

AC:

AN:

3356

European-Finnish (FIN)

AF:

0.00

AC:

AN:

7790

Middle Eastern (MID)

AF:

0.00407

AC:

AN:

246

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

57348

Other (OTH)

AF:

0.00

AC:

AN:

1590

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.225

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.90

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over