chr14-36662975-G-T
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM2PM5PP3_Strong
The NM_001372076.1(PAX9):c.83G>T(p.Arg28Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,264 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R28P) has been classified as Pathogenic.
Frequency
Consequence
NM_001372076.1 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 | UniProt |
---|---|---|---|---|---|---|---|
PAX9 | NM_001372076.1 | c.83G>T | p.Arg28Leu | missense_variant | 2/4 | ENST00000361487.7 | |
PAX9 | NM_006194.4 | c.83G>T | p.Arg28Leu | missense_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PAX9 | ENST00000361487.7 | c.83G>T | p.Arg28Leu | missense_variant | 2/4 | 1 | NM_001372076.1 | P1 | |
PAX9 | ENST00000402703.6 | c.83G>T | p.Arg28Leu | missense_variant | 3/5 | 5 | P1 | ||
PAX9 | ENST00000555639.2 | c.83G>T | p.Arg28Leu | missense_variant | 3/3 | 5 | |||
PAX9 | ENST00000554201.1 | n.402G>T | non_coding_transcript_exon_variant | 1/3 | 2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461264Hom.: 0 Cov.: 37 AF XY: 0.00000138 AC XY: 1AN XY: 726944
GnomAD4 genome Cov.: 33
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at