chr1-98956617-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001037317.2(PLPPR5):c.362G>A(p.Arg121Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000114 in 1,577,924 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.362G>A | p.Arg121Gln | missense_variant | Exon 2 of 6 | ENST00000263177.5 | NP_001032394.1 | |
PLPPR5 | NM_001010861.3 | c.362G>A | p.Arg121Gln | missense_variant | Exon 2 of 6 | NP_001010861.1 | ||
PLPPR5 | XM_011540838.4 | c.314G>A | p.Arg105Gln | missense_variant | Exon 3 of 7 | XP_011539140.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PLPPR5 | ENST00000263177.5 | c.362G>A | p.Arg121Gln | missense_variant | Exon 2 of 6 | 1 | NM_001037317.2 | ENSP00000263177.4 | ||
PLPPR5 | ENST00000370188.7 | c.362G>A | p.Arg121Gln | missense_variant | Exon 2 of 6 | 1 | ENSP00000359207.3 | |||
PLPPR5 | ENST00000672681.1 | c.362G>A | p.Arg121Gln | missense_variant | Exon 2 of 7 | ENSP00000500930.1 | ||||
PLPPR5 | ENST00000696571.1 | c.197G>A | p.Arg66Gln | missense_variant | Exon 3 of 7 | ENSP00000512726.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152144Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.00000459 AC: 1AN: 218086Hom.: 0 AF XY: 0.00000841 AC XY: 1AN XY: 118864
GnomAD4 exome AF: 0.0000119 AC: 17AN: 1425780Hom.: 0 Cov.: 30 AF XY: 0.00000988 AC XY: 7AN XY: 708436
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152144Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74312
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.362G>A (p.R121Q) alteration is located in exon 2 (coding exon 2) of the PLPPR5 gene. This alteration results from a G to A substitution at nucleotide position 362, causing the arginine (R) at amino acid position 121 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