chr11-74456155-A-AATATATATATATATATATATATATAT

Variant names:

• chr11-74456155-A-AATATATATATATATATATATATATAT
• rs113583236
• NM_005472.5:c.*1096_*1097insATATATATATATATATATATATATAT

Variant summary

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

The NM_005472.5(KCNE3):​c.*1096_*1097insATATATATATATATATATATATATAT 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 0.0024 (5 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 275 AD gene.

Transcripts

RefSeq

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

Frequencies

GnomAD3 genomes AF: 0.00243 AC: 275 AN: 113022 Hom.: 5 Cov.: 0

Gnomad AFR AF: 0.00125

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00193

Gnomad ASJ AF: 0.00743

Gnomad EAS AF: 0.00278

Gnomad SAS AF: 0.00394

Gnomad FIN AF: 0.000240

Gnomad MID AF: 0.00450

Gnomad NFE AF: 0.00304

Gnomad OTH AF: 0.00539

GnomAD4 exome Cov.: 0

GnomAD4 genome AF: 0.00243 AC: 275 AN: 113046 Hom.: 5 Cov.: 0 AF XY: 0.00238 AC XY: 127 AN XY: 53310

Gnomad4 AFR AF: 0.00125

Gnomad4 AMR AF: 0.00193

Gnomad4 ASJ AF: 0.00743

Gnomad4 EAS AF: 0.00279

Gnomad4 SAS AF: 0.00397

Gnomad4 FIN AF: 0.000240

Gnomad4 NFE AF: 0.00304

Gnomad4 OTH AF: 0.00534

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;