rs121908840
Variant summary
Our verdict is Pathogenic. Variant got 19 ACMG points: 19P and 0B. PM1PM2PM5PP2PP3_StrongPP5_Very_Strong
The NM_003722.5(TP63):c.953G>A(p.Arg318His) 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. 13/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R318Q) has been classified as Likely pathogenic.
Frequency
Consequence
NM_003722.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 19 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TP63 | NM_003722.5 | c.953G>A | p.Arg318His | missense_variant | Exon 7 of 14 | ENST00000264731.8 | NP_003713.3 | |
TP63 | NM_001114980.2 | c.671G>A | p.Arg224His | missense_variant | Exon 5 of 12 | ENST00000354600.10 | NP_001108452.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TP63 | ENST00000264731.8 | c.953G>A | p.Arg318His | missense_variant | Exon 7 of 14 | 1 | NM_003722.5 | ENSP00000264731.3 | ||
TP63 | ENST00000354600.10 | c.671G>A | p.Arg224His | missense_variant | Exon 5 of 12 | 1 | NM_001114980.2 | ENSP00000346614.5 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Ectrodactyly, ectodermal dysplasia, and cleft lip-palate syndrome 3 Pathogenic:3
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Same or different nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000006533, PMID:10535733). A different missense change at the same codon has been reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000650760, PMID:19903181,11462173,11462173). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.948>=0.6, 3CNET: 0.993>=0.75). A missense variant is a common mechanism associated with Ectrodactyly, ectodermal dysplasia, and cleft lip/palate syndrome 3. It is not observed in the gnomAD v2.1.1 dataset. Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline. -
not provided Pathogenic:2
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Published functional studies demonstrate an inhibitory effect of the variant on the wildtype p63 protein, and mouse models for this variant display an ectrodactyly phenotype (PMID: 18626511, 23775923); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Also known as R279H; This variant is associated with the following publications: (PMID: 21652629, 34321610, 23355676, 19353588, 23775923, 20543567, 30566872, 17224651, 18626511, 10535733, 23431748, 11903230) -
TP63-Related Spectrum Disorders Pathogenic:1
This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 318 of the TP63 protein (p.Arg318His). For these reasons, this variant has been classified as Pathogenic. This variant disrupts the p.Arg318 amino acid residue in TP63. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 11462173, 21652629). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. Experimental studies have shown that this missense change affects TP63 function (PMID: 18326838, 23775923). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt TP63 protein function. ClinVar contains an entry for this variant (Variation ID: 6533). This variant is also known as p.Arg279His. This missense change has been observed in individuals with split hand–split foot malformation (SHFM) or ectrodactyly, ectodermal dysplasia and facial clefts syndrome (EEC syndrome) (PMID: 10535733, 11462173, 12525544, 23355676, 23431748). It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency). -
Rapp-Hodgkin syndrome Pathogenic:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at