Variant Info - hg38

11-2797090-2869333-DEL

Gene: KCNQ1

pLI: 2.45e-05

Haploinsufficiency: 3

Transcript: NM_181798.1

Exon: 16/16

Intron: 15/15

PVS1 Flowchart

• Deletion (single exon to full gene)
  • Single to multi exon deletion
Preserves reading frame
    • Role of region in protein
function is unknown #1
      • LoF variants in this exon are not frequent
in the general population #2 and exon is
present in biologically-relevant transcript(s)
        • Variant removes >10% of protein
          • Strong

#1 Neither mutational hotspot nor functional domain is found.
#2 Maximum LOF population frequency in exon 16 of NM_000218.3 is 3.29e-04, lower than the threshold (0.1%) we pre-defined.

Disease Mechanism

Gene	Disease	Clinical Validity	Disease Mechanism Consideration	Adjusted Strength
KCNQ1	Jervell and Lange-Nielsen syndrome	Definitive	No Decrease	Strong
KCNQ1	short QT syndrome	Strong	No Decrease	Strong
KCNQ1	hypertrophic cardiomyopathy	No Known Disease Relationship	Not applicable	Unmet
KCNQ1	long QT syndrome	Definitive	No Decrease	Strong