8-9141164-C-T
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_024607.4(PPP1R3B):c.488G>A(p.Arg163Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,892 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_024607.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PPP1R3B | NM_024607.4 | c.488G>A | p.Arg163Lys | missense_variant | Exon 2 of 2 | ENST00000310455.4 | NP_078883.2 | |
PPP1R3B | NM_001201329.2 | c.488G>A | p.Arg163Lys | missense_variant | Exon 2 of 2 | NP_001188258.1 | ||
PPP1R3B | XM_006716253.4 | c.488G>A | p.Arg163Lys | missense_variant | Exon 2 of 2 | XP_006716316.1 | ||
PPP1R3B | XM_047422235.1 | c.488G>A | p.Arg163Lys | missense_variant | Exon 2 of 2 | XP_047278191.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251464Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135902
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461892Hom.: 0 Cov.: 35 AF XY: 0.00000138 AC XY: 1AN XY: 727246
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.488G>A (p.R163K) alteration is located in exon 2 (coding exon 1) of the PPP1R3B gene. This alteration results from a G to A substitution at nucleotide position 488, causing the arginine (R) at amino acid position 163 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