11-74456155-AATATATATATATAT-AATATATATATATATATAT

Variant names:

• chr11-74456155-A-AATAT
• rs113583236
• NM_005472.5:c.*1093_*1096dupATAT

Variant summary

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

The NM_005472.5(KCNE3):​c.*1093_*1096dupATAT 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 0.00060 (0 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 Likely_benign. Variant got -4 ACMG points.

• BS2: High AC in GnomAd4 at 68 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
KCNE3	NM_005472.5	c.*1093_*1096dupATAT		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.*1093_*1096dupATAT		3_prime_UTR_variant	Exon 3 of 3	1	NM_005472.5	ENSP00000310557.4
ENSG00000254928	ENST00000530510.1	n.425+405_425+408dupTATA		intron_variant	Intron 1 of 1	2
ENSG00000254631	ENST00000533008.1	n.155-28000_155-27997dupTATA		intron_variant	Intron 2 of 3	3

Frequencies

GnomAD3 genomes AF: 0.000601 AC: 68 AN: 113096 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.000814

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00125

Gnomad ASJ AF: 0.000707

Gnomad EAS AF: 0.000309

Gnomad SAS AF: 0.00121

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000382

Gnomad OTH AF: 0.00

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: 0.000601 AC: 68 AN: 113120 Hom.: 0 Cov.: 0 AF XY: 0.000600 AC XY: 32 AN XY: 53344

Gnomad4 AFR AF: 0.000813

Gnomad4 AMR AF: 0.00125

Gnomad4 ASJ AF: 0.000707

Gnomad4 EAS AF: 0.000310

Gnomad4 SAS AF: 0.00122

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000382

Gnomad4 OTH AF: 0.00

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;