rs121909656
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM2PM5PP3_StrongPP5
The ENST00000261937.11(FLT4):c.3316G>A(p.Glu1106Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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. E1106D) has been classified as Pathogenic.
Frequency
Consequence
ENST00000261937.11 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FLT4 | NM_182925.5 | c.3316G>A | p.Glu1106Lys | missense_variant | 24/30 | ENST00000261937.11 | NP_891555.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FLT4 | ENST00000261937.11 | c.3316G>A | p.Glu1106Lys | missense_variant | 24/30 | 1 | NM_182925.5 | ENSP00000261937 | P1 |
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD4 exome Cov.: 32
GnomAD4 genome Cov.: 34
ClinVar
Submissions by phenotype
Hereditary lymphedema type I Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jan 01, 2006 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at