14-36666519-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PP3_Moderate
The NM_001372076.1(PAX9):c.689G>T(p.Arg230Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000062 in 1,451,064 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R230H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001372076.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PAX9 | NM_001372076.1 | c.689G>T | p.Arg230Leu | missense_variant | 3/4 | ENST00000361487.7 | |
PAX9 | NM_006194.4 | c.689G>T | p.Arg230Leu | missense_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PAX9 | ENST00000361487.7 | c.689G>T | p.Arg230Leu | missense_variant | 3/4 | 1 | NM_001372076.1 | P1 | |
PAX9 | ENST00000402703.6 | c.689G>T | p.Arg230Leu | missense_variant | 4/5 | 5 | P1 | ||
PAX9 | ENST00000554201.1 | n.1008G>T | non_coding_transcript_exon_variant | 2/3 | 2 | ||||
PAX9 | ENST00000557107.1 | n.530G>T | non_coding_transcript_exon_variant | 1/4 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 0.00000620 AC: 9AN: 1451064Hom.: 0 Cov.: 30 AF XY: 0.00000971 AC XY: 7AN XY: 720790
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Partial congenital absence of teeth Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | May 20, 2018 | This sequence change replaces arginine with leucine at codon 230 of the PAX9 protein (p.Arg230Leu). The arginine residue is highly conserved and there is a moderate physicochemical difference between arginine and leucine. This variant is not present in population databases (ExAC no frequency). This variant has not been reported in the literature in individuals with PAX9-related disease. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C65"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Mar 06, 2023 | In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at