chr1-98914823-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001037317.2(PLPPR5):c.896G>A(p.Arg299Gln) variant causes a missense change. The variant allele was found at a frequency of 0.0000217 in 1,612,996 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001037317.2 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 |
---|---|---|---|---|---|---|---|---|
PLPPR5 | NM_001037317.2 | c.896G>A | p.Arg299Gln | missense_variant | Exon 5 of 6 | ENST00000263177.5 | NP_001032394.1 | |
PLPPR5 | NM_001010861.3 | c.896G>A | p.Arg299Gln | missense_variant | Exon 5 of 6 | NP_001010861.1 | ||
PLPPR5 | XM_011540838.4 | c.848G>A | p.Arg283Gln | missense_variant | Exon 6 of 7 | XP_011539140.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLPPR5 | ENST00000263177.5 | c.896G>A | p.Arg299Gln | missense_variant | Exon 5 of 6 | 1 | NM_001037317.2 | ENSP00000263177.4 | ||
PLPPR5 | ENST00000370188.7 | c.896G>A | p.Arg299Gln | missense_variant | Exon 5 of 6 | 1 | ENSP00000359207.3 | |||
PLPPR5 | ENST00000672681.1 | c.896G>A | p.Arg299Gln | missense_variant | Exon 5 of 7 | ENSP00000500930.1 | ||||
PLPPR5 | ENST00000696571.1 | c.731G>A | p.Arg244Gln | missense_variant | Exon 6 of 7 | ENSP00000512726.1 |
Frequencies
GnomAD3 genomes AF: 0.0000132 AC: 2AN: 152018Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000798 AC: 2AN: 250658Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135512
GnomAD4 exome AF: 0.0000226 AC: 33AN: 1460978Hom.: 0 Cov.: 30 AF XY: 0.0000220 AC XY: 16AN XY: 726822
GnomAD4 genome AF: 0.0000132 AC: 2AN: 152018Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74252
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.896G>A (p.R299Q) alteration is located in exon 5 (coding exon 5) of the PLPPR5 gene. This alteration results from a G to A substitution at nucleotide position 896, causing the arginine (R) at amino acid position 299 to be replaced by a glutamine (Q). 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