rs387906778

chr11-128911745-A-G

Variant summary

Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM1 PM2 PM5 PP3_Strong PP5

The NM_000890.5(KCNJ5):c.472A>G(p.Thr158Ala) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T158R) has been classified as Likely pathogenic.

• Frequency: Genomes: not found (cov: 32)
• Consequence: KCNJ5 NM_000890.5 missense
• Clinical Significance: Pathogenic no assertion criteria provided P:2 O:1
• Conservation: PhyloP100: 9.32

Genes affected

KCNJ5 (HGNC:6266): (potassium inwardly rectifying channel subfamily J member 5) This gene encodes an integral membrane protein which belongs to one of seven subfamilies of inward-rectifier potassium channel proteins called potassium channel subfamily J. The encoded protein is a subunit of the potassium channel which is homotetrameric. It is controlled by G-proteins and has a greater tendency to allow potassium to flow into a cell rather than out of a cell. Naturally occurring mutations in this gene are associated with aldosterone-producing adenomas. [provided by RefSeq, Aug 2017]

ACMG classification

Verdict is Pathogenic. Variant got 11 ACMG points.

• PM1: In a hotspot region, there are 2 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 7 uncertain in NM_000890.5
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr11-128911746-C-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 1467663.Status of the report is criteria_provided_single_submitter, 1 stars.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.973
• PP5: Variant 11-128911745-A-G is Pathogenic according to our data. Variant chr11-128911745-A-G is described in ClinVar as [Pathogenic]. Clinvar id is 30125.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
KCNJ5	NM_000890.5	c.472A>G	p.Thr158Ala	missense_variant	2/3	ENST00000529694.6
KCNJ5	NM_001354169.2	c.472A>G	p.Thr158Ala	missense_variant	3/4
KCNJ5	XM_011542810.4	c.472A>G	p.Thr158Ala	missense_variant	2/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
KCNJ5	ENST00000529694.6	c.472A>G	p.Thr158Ala	missense_variant	2/3	1	NM_000890.5	P1
KCNJ5	ENST00000338350.4	c.472A>G	p.Thr158Ala	missense_variant	3/4	1		P1
KCNJ5	ENST00000533599.1	c.472A>G	p.Thr158Ala	missense_variant	1/2	1		P1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 58

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:2 Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Aldosterone-producing adrenal adenoma, somatic Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Mar 25, 2014

- -

Familial hyperaldosteronism type III Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Mar 25, 2014

- -

Andersen Tawil syndrome Other:1

not provided, no classification provided

literature only

GeneReviews

-

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.79
BayesDel_addAF	Pathogenic	0.50	D
BayesDel_noAF	Pathogenic	0.48
Cadd	Uncertain	24
Dann	Uncertain	0.99
DEOGEN2	Pathogenic	0.94	D;D;D
Eigen	Uncertain	0.24
Eigen_PC	Uncertain	0.33
FATHMM_MKL	Pathogenic	0.99	D
M_CAP	Uncertain	0.25	D
MetaRNN	Pathogenic	0.97	D;D;D
MetaSVM	Uncertain	0.72	D
MutationAssessor	Pathogenic	3.1	M;M;M
MutationTaster	Benign	1.0	D;D;D
PrimateAI	Uncertain	0.76	T
PROVEAN	Pathogenic	-4.6	D;D;D
REVEL	Pathogenic	0.91
Sift	Uncertain	0.0040	D;D;D
Sift4G	Uncertain	0.018	D;D;D
Polyphen		0.082	B;B;B
Vest4		0.95
MutPred		0.89		Loss of ubiquitination at K160 (P = 0.0821);Loss of ubiquitination at K160 (P = 0.0821);Loss of ubiquitination at K160 (P = 0.0821);
MVP		0.95
MPC		0.50
ClinPred		0.99	D
GERP RS		5.5
Varity_R		0.77
gMVP		0.97

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

Other links and lift over

dbSNP: rs387906778; hg19: chr11-128781640; COSMIC: COSV57963867;