NM_020315.5:c.695G>T
Variant summary
Our verdict is Uncertain significance. The variant received 1 ACMG points: 1P and 0B. PP3
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
Publications
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ACMG classification
Our verdict: Uncertain_significance. The variant received 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PDXP | NM_020315.5 | c.695G>T | p.Arg232Leu | missense_variant | Exon 2 of 2 | ENST00000215904.7 | NP_064711.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PDXP | ENST00000215904.7 | c.695G>T | p.Arg232Leu | missense_variant | Exon 2 of 2 | 1 | NM_020315.5 | ENSP00000215904.6 | ||
ENSG00000285304 | ENST00000451997.6 | c.1622G>T | p.Arg541Leu | missense_variant | Exon 17 of 17 | 2 | ENSP00000401076.2 | |||
PDXP | ENST00000403251.1 | c.44G>T | p.Arg15Leu | missense_variant | Exon 2 of 2 | 2 | ENSP00000385336.1 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152198Hom.: 0 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.0000557 AC: 14AN: 251344 AF XY: 0.0000736 show subpopulations
GnomAD4 exome AF: 0.0000746 AC: 109AN: 1461778Hom.: 0 Cov.: 32 AF XY: 0.0000866 AC XY: 63AN XY: 727202 show subpopulations
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152198Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74374 show subpopulations
ClinVar
Submissions by phenotype
not specified Uncertain:1
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