1-204409645-CTTT-C
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PM4_Supporting
The NM_032833.5(PPP1R15B):c.1764_1766delAAA(p.Lys589del) variant causes a disruptive inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000141 in 1,613,984 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032833.5 disruptive_inframe_deletion
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PPP1R15B | NM_032833.5 | c.1764_1766delAAA | p.Lys589del | disruptive_inframe_deletion | Exon 1 of 2 | ENST00000367188.5 | NP_116222.4 | |
PPP1R15B | XM_005245551.6 | c.1764_1766delAAA | p.Lys589del | disruptive_inframe_deletion | Exon 1 of 3 | XP_005245608.2 | ||
PPP1R15B | XM_047432518.1 | c.1764_1766delAAA | p.Lys589del | disruptive_inframe_deletion | Exon 1 of 3 | XP_047288474.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152100Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000557 AC: 14AN: 251470Hom.: 0 AF XY: 0.0000589 AC XY: 8AN XY: 135912
GnomAD4 exome AF: 0.000142 AC: 207AN: 1461884Hom.: 0 AF XY: 0.000135 AC XY: 98AN XY: 727240
GnomAD4 genome AF: 0.000138 AC: 21AN: 152100Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74302
ClinVar
Submissions by phenotype
not provided Uncertain:1
This variant, c.1764_1766del, results in the deletion of 1 amino acid(s) of the PPP1R15B protein (p.Lys589del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs764878882, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with PPP1R15B-related conditions. ClinVar contains an entry for this variant (Variation ID: 2890553). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at