19-812682-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001270366.2(PLPPR3):c.2045G>C(p.Arg682Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000801 in 1,048,856 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001270366.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PLPPR3 | NM_001270366.2 | c.2045G>C | p.Arg682Pro | missense_variant | Exon 8 of 8 | ENST00000520876.8 | NP_001257295.1 | |
PLPPR3 | NM_024888.3 | c.2129G>C | p.Arg710Pro | missense_variant | Exon 7 of 7 | NP_079164.1 | ||
PLPPR3 | XM_011528317.4 | c.2129G>C | p.Arg710Pro | missense_variant | Exon 7 of 7 | XP_011526619.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLPPR3 | ENST00000520876.8 | c.2045G>C | p.Arg682Pro | missense_variant | Exon 8 of 8 | 1 | NM_001270366.2 | ENSP00000430297.1 | ||
PLPPR3 | ENST00000359894.6 | c.2129G>C | p.Arg710Pro | missense_variant | Exon 7 of 7 | 1 | ENSP00000352962.2 |
Frequencies
GnomAD3 genomes AF: 0.000123 AC: 18AN: 146598Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.0000731 AC: 66AN: 902258Hom.: 0 Cov.: 34 AF XY: 0.0000851 AC XY: 36AN XY: 422958
GnomAD4 genome AF: 0.000123 AC: 18AN: 146598Hom.: 0 Cov.: 32 AF XY: 0.000196 AC XY: 14AN XY: 71282
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2129G>C (p.R710P) alteration is located in exon 7 (coding exon 6) of the PLPPR3 gene. This alteration results from a G to C substitution at nucleotide position 2129, causing the arginine (R) at amino acid position 710 to be replaced by a proline (P). 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