chr22-37665675-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_020315.5(PDXP):c.695G>T(p.Arg232Leu) variant causes a missense change. The variant allele was found at a frequency of 0.0000744 in 1,613,976 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. R232H) has been classified as Uncertain significance.
Frequency
Consequence
NM_020315.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PDXP | NM_020315.5 | c.695G>T | p.Arg232Leu | missense_variant | 2/2 | ENST00000215904.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PDXP | ENST00000215904.7 | c.695G>T | p.Arg232Leu | missense_variant | 2/2 | 1 | NM_020315.5 | P1 | |
PDXP | ENST00000403251.1 | c.44G>T | p.Arg15Leu | missense_variant | 2/2 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152198Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251344Hom.: 0 AF XY: 0.0000736 AC XY: 10AN XY: 135908
GnomAD4 exome AF: 0.0000746 AC: 109AN: 1461778Hom.: 0 Cov.: 32 AF XY: 0.0000866 AC XY: 63AN XY: 727202
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152198Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74374
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 03, 2022 | The c.695G>T (p.R232L) alteration is located in exon 2 (coding exon 2) of the PDXP gene. This alteration results from a G to T substitution at nucleotide position 695, causing the arginine (R) at amino acid position 232 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at