chr11-74456155-A-AATATATATATATATATATATATATATATATAT

Variant names:

• chr11-74456155-A-AATATATATATATATATATATATATATATATAT
• rs113583236
• NM_005472.5:c.*1096_*1097insATATATATATATATATATATATATATATATAT

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The NM_005472.5(KCNE3):​c.*1096_*1097insATATATATATATATATATATATATATATATAT variant causes a 3 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 0.00025 (1 hom., cov: 0)
• Consequence: KCNE3 NM_005472.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.296

Genes affected

KCNE3 (HGNC:6243): (potassium voltage-gated channel subfamily E regulatory subunit 3) Voltage-gated potassium (Kv) channels represent the most complex class of voltage-gated ion channels from both functional and structural standpoints. Their diverse functions include regulating neurotransmitter release, heart rate, insulin secretion, neuronal excitability, epithelial electrolyte transport, smooth muscle contraction, and cell volume. This gene encodes a member of the potassium channel, voltage-gated, isk-related subfamily. This member is a type I membrane protein, and a beta subunit that assembles with a potassium channel alpha-subunit to modulate the gating kinetics and enhance stability of the multimeric complex. This gene is prominently expressed in the kidney. A missense mutation in this gene is associated with hypokalemic periodic paralysis. [provided by RefSeq, Jul 2008]

ENSG00000254928 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS2: High AC in GnomAd4 at 28 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KCNE3	NM_005472.5	c.*1096_*1097insATATATATATATATATATATATATATATATAT		3_prime_UTR_variant	Exon 3 of 3	ENST00000310128.9	NP_005463.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
KCNE3	ENST00000310128	c.*1096_*1097insATATATATATATATATATATATATATATATAT		3_prime_UTR_variant	Exon 3 of 3	1	NM_005472.5	ENSP00000310557.4
ENSG00000254928	ENST00000530510.1	n.425+408_425+409insTATATATATATATATATATATATATATATATA		intron_variant	Intron 1 of 1	2
ENSG00000254631	ENST00000533008.1	n.155-27997_155-27996insTATATATATATATATATATATATATATATATA		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.000248 AC: 28 AN: 113082 Hom.: 1 Cov.: 0

Gnomad AFR AF: 0.0000582

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000482

Gnomad ASJ AF: 0.00141

Gnomad EAS AF: 0.000617

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000268

Gnomad OTH AF: 0.000674

GnomAD4 exome Cov.: 0

GnomAD4 genome AF: 0.000248 AC: 28 AN: 113106 Hom.: 1 Cov.: 0 AF XY: 0.000281 AC XY: 15 AN XY: 53342

Gnomad4 AFR AF: 0.0000581

Gnomad4 AMR AF: 0.000481

Gnomad4 ASJ AF: 0.00141

Gnomad4 EAS AF: 0.000620

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000268

Gnomad4 OTH AF: 0.000668

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: rs113583236; hg19: chr11-74167200;