rs1057519584
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM1PM2PP3PP5
The NM_000218.3(KCNQ1):c.835T>A(p.Phe279Ile) variant causes a missense change. The variant allele was found at a frequency of 0.00000137 in 1,461,494 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. F279C) has been classified as Uncertain significance.
Frequency
Consequence
NM_000218.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNQ1 | NM_000218.3 | c.835T>A | p.Phe279Ile | missense_variant | 6/16 | ENST00000155840.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNQ1 | ENST00000155840.12 | c.835T>A | p.Phe279Ile | missense_variant | 6/16 | 1 | NM_000218.3 | P1 | |
KCNQ1 | ENST00000335475.6 | c.454T>A | p.Phe152Ile | missense_variant | 6/16 | 1 | |||
KCNQ1 | ENST00000496887.7 | c.574T>A | p.Phe192Ile | missense_variant | 7/16 | 5 | |||
KCNQ1 | ENST00000646564.2 | c.478-10535T>A | intron_variant |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461494Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 727064
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Short QT syndrome type 2 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Feb 09, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at