NM_005472.5:c.*1079_*1096dupATATATATATATATATAT

Variant names:

• chr11-74456155-A-AATATATATATATATATAT
• rs113583236
• NM_005472.5:c.*1079_*1096dupATATATATATATATATAT

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_005472.5(KCNE3):​c.*1079_*1096dupATATATATATATATATAT 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 0.036 (171 hom., cov: 0)
  • Failed GnomAD Quality Control
• 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 Benign. Variant got -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0506 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KCNE3	NM_005472.5	c.*1079_*1096dupATATATATATATATATAT		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.*1079_*1096dupATATATATATATATATAT		3_prime_UTR_variant	Exon 3 of 3	1	NM_005472.5	ENSP00000310557.4
ENSG00000254928	ENST00000530510.1	n.425+391_425+408dupTATATATATATATATATA		intron_variant	Intron 1 of 1	2
ENSG00000254631	ENST00000533008.1	n.155-28014_155-27997dupTATATATATATATATATA		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.0359 AC: 4037 AN: 112550 Hom.: 171 Cov.: 0

Gnomad AFR AF: 0.0136

Gnomad AMI AF: 0.0180

Gnomad AMR AF: 0.0301

Gnomad ASJ AF: 0.0397

Gnomad EAS AF: 0.0426

Gnomad SAS AF: 0.0320

Gnomad FIN AF: 0.0201

Gnomad MID AF: 0.0367

Gnomad NFE AF: 0.0523

Gnomad OTH AF: 0.0529

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.0359 AC: 4036 AN: 112572 Hom.: 171 Cov.: 0 AF XY: 0.0334 AC XY: 1772 AN XY: 53024

Gnomad4 AFR AF: 0.0136

Gnomad4 AMR AF: 0.0302

Gnomad4 ASJ AF: 0.0397

Gnomad4 EAS AF: 0.0428

Gnomad4 SAS AF: 0.0322

Gnomad4 FIN AF: 0.0201

Gnomad4 NFE AF: 0.0523

Gnomad4 OTH AF: 0.0524

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;