rs368787836
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 1P and 5B. PP3BS1_SupportingBS2
The NM_001372076.1(PAX9):c.689G>A(p.Arg230His) variant causes a missense change. The variant allele was found at a frequency of 0.0000312 in 1,603,272 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. R230L) has been classified as Uncertain significance.
Frequency
Consequence
NM_001372076.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PAX9 | NM_001372076.1 | c.689G>A | p.Arg230His | missense_variant | 3/4 | ENST00000361487.7 | |
PAX9 | NM_006194.4 | c.689G>A | p.Arg230His | missense_variant | 4/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PAX9 | ENST00000361487.7 | c.689G>A | p.Arg230His | missense_variant | 3/4 | 1 | NM_001372076.1 | P1 | |
PAX9 | ENST00000402703.6 | c.689G>A | p.Arg230His | missense_variant | 4/5 | 5 | P1 | ||
PAX9 | ENST00000554201.1 | n.1008G>A | non_coding_transcript_exon_variant | 2/3 | 2 | ||||
PAX9 | ENST00000557107.1 | n.530G>A | non_coding_transcript_exon_variant | 1/4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152218Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000223 AC: 5AN: 224640Hom.: 0 AF XY: 0.0000164 AC XY: 2AN XY: 122054
GnomAD4 exome AF: 0.0000303 AC: 44AN: 1451054Hom.: 0 Cov.: 30 AF XY: 0.0000277 AC XY: 20AN XY: 720788
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152218Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74350
ClinVar
Submissions by phenotype
Tooth agenesis, selective, 3 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 13, 2018 | This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at