chr19-812632-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001270366.2(PLPPR3):c.2095G>A(p.Glu699Lys) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. 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 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PLPPR3 | NM_001270366.2 | c.2095G>A | p.Glu699Lys | missense_variant | Exon 8 of 8 | ENST00000520876.8 | NP_001257295.1 | |
PLPPR3 | NM_024888.3 | c.2179G>A | p.Glu727Lys | missense_variant | Exon 7 of 7 | NP_079164.1 | ||
PLPPR3 | XM_011528317.4 | c.2179G>A | p.Glu727Lys | 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.2095G>A | p.Glu699Lys | missense_variant | Exon 8 of 8 | 1 | NM_001270366.2 | ENSP00000430297.1 | ||
PLPPR3 | ENST00000359894.6 | c.2179G>A | p.Glu727Lys | missense_variant | Exon 7 of 7 | 1 | ENSP00000352962.2 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 961436Hom.: 0 Cov.: 35 AF XY: 0.00 AC XY: 0AN XY: 463536
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2179G>A (p.E727K) alteration is located in exon 7 (coding exon 6) of the PLPPR3 gene. This alteration results from a G to A substitution at nucleotide position 2179, causing the glutamic acid (E) at amino acid position 727 to be replaced by a lysine (K). 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