3-189864349-A-G
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM1PM2PP2PP3_StrongPP5
The NM_003722.5(TP63):c.697A>G(p.Lys233Glu) 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. K233T) has been classified as Uncertain significance.
Frequency
Consequence
NM_003722.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TP63 | NM_003722.5 | c.697A>G | p.Lys233Glu | missense_variant | 5/14 | ENST00000264731.8 | |
TP63 | NM_001114980.2 | c.415A>G | p.Lys139Glu | missense_variant | 3/12 | ENST00000354600.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TP63 | ENST00000264731.8 | c.697A>G | p.Lys233Glu | missense_variant | 5/14 | 1 | NM_003722.5 | P4 | |
TP63 | ENST00000354600.10 | c.415A>G | p.Lys139Glu | missense_variant | 3/12 | 1 | NM_001114980.2 | A1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Split hand-foot malformation 4 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jul 01, 2000 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at