rs1555316711
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_001372076.1(PAX9):c.217G>T(p.Gly73Cys) 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. 12/21 in silico tools predict a damaging 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. G73V) 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_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PAX9 | NM_001372076.1 | c.217G>T | p.Gly73Cys | missense_variant | 2/4 | ENST00000361487.7 | |
PAX9 | NM_006194.4 | c.217G>T | p.Gly73Cys | missense_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PAX9 | ENST00000361487.7 | c.217G>T | p.Gly73Cys | missense_variant | 2/4 | 1 | NM_001372076.1 | P1 | |
PAX9 | ENST00000402703.6 | c.217G>T | p.Gly73Cys | missense_variant | 3/5 | 5 | P1 | ||
PAX9 | ENST00000555639.2 | c.217G>T | p.Gly73Cys | missense_variant | 3/3 | 5 | |||
PAX9 | ENST00000554201.1 | n.536G>T | non_coding_transcript_exon_variant | 1/3 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome Cov.: 37
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 16, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at