4-54727444-T-A
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM2PM5PP2PP3_ModeratePP5
The NM_000222.3(KIT):c.1676T>A(p.Val559Asp) 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. V559G) has been classified as Likely pathogenic.
Frequency
Consequence
NM_000222.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
KIT | NM_000222.3 | c.1676T>A | p.Val559Asp | missense_variant | 11/21 | ENST00000288135.6 | NP_000213.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
KIT | ENST00000288135.6 | c.1676T>A | p.Val559Asp | missense_variant | 11/21 | 1 | NM_000222.3 | ENSP00000288135.6 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 33
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Gastrointestinal stromal tumor Pathogenic:1Other:1
-, no assertion criteria provided | research | National Institute of Cancer Research, National Health Research Institutes | - | the literature - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Jan 23, 1998 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at