19-812820-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001270366.2(PLPPR3):c.1907G>C(p.Gly636Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000172 in 1,107,584 control chromosomes in the GnomAD database, with no homozygous occurrence. 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.1907G>C | p.Gly636Ala | missense_variant | Exon 8 of 8 | ENST00000520876.8 | NP_001257295.1 | |
PLPPR3 | NM_024888.3 | c.1991G>C | p.Gly664Ala | missense_variant | Exon 7 of 7 | NP_079164.1 | ||
PLPPR3 | XM_011528317.4 | c.1991G>C | p.Gly664Ala | 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.1907G>C | p.Gly636Ala | missense_variant | Exon 8 of 8 | 1 | NM_001270366.2 | ENSP00000430297.1 | ||
PLPPR3 | ENST00000359894.6 | c.1991G>C | p.Gly664Ala | missense_variant | Exon 7 of 7 | 1 | ENSP00000352962.2 |
Frequencies
GnomAD3 genomes AF: 0.0000951 AC: 14AN: 147164Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000521 AC: 5AN: 960420Hom.: 0 Cov.: 34 AF XY: 0.00000662 AC XY: 3AN XY: 453468
GnomAD4 genome AF: 0.0000951 AC: 14AN: 147164Hom.: 0 Cov.: 32 AF XY: 0.0000977 AC XY: 7AN XY: 71624
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1991G>C (p.G664A) 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 1991, causing the glycine (G) at amino acid position 664 to be replaced by an alanine (A). 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