rs121918498
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PS1_ModeratePM2PM5PP2PP3PP5_Moderate
The NM_000141.5(FGFR2):c.755_756delCGinsTT(p.Ser252Phe) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely pathogenic in UniProt. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S252L) has been classified as Pathogenic.
Frequency
Consequence
NM_000141.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FGFR2 | ENST00000358487.10 | c.755_756delCGinsTT | p.Ser252Phe | missense_variant | 1 | NM_000141.5 | ENSP00000351276.6 | |||
FGFR2 | ENST00000457416.7 | c.755_756delCGinsTT | p.Ser252Phe | missense_variant | 1 | ENSP00000410294.2 | ||||
FGFR2 | ENST00000369056.5 | c.755_756delCGinsTT | p.Ser252Phe | missense_variant | 1 | ENSP00000358052.1 | ||||
FGFR2 | ENST00000369058.7 | c.755_756delCGinsTT | p.Ser252Phe | missense_variant | 1 | ENSP00000358054.3 | ||||
FGFR2 | ENST00000613048.4 | c.488_489delCGinsTT | p.Ser163Phe | missense_variant | 5 | ENSP00000484154.1 | ||||
FGFR2 | ENST00000369059.5 | c.410_411delCGinsTT | p.Ser137Phe | missense_variant | 5 | ENSP00000358055.1 | ||||
FGFR2 | ENST00000360144.7 | c.488_489delCGinsTT | p.Ser163Phe | missense_variant | 2 | ENSP00000353262.3 | ||||
FGFR2 | ENST00000478859.5 | c.71_72delCGinsTT | p.Ser24Phe | missense_variant | 1 | ENSP00000474011.1 | ||||
FGFR2 | ENST00000369061.8 | c.749-4844_749-4843delCGinsTT | intron_variant | Intron 5 of 14 | 1 | ENSP00000358057.4 | ||||
FGFR2 | ENST00000604236.5 | n.410_411delCGinsTT | non_coding_transcript_exon_variant | Exon 5 of 17 | 1 | ENSP00000474109.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Acrocephalosyndactyly type I Pathogenic:2Other:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at