rs387907103
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_017813.5(BPNT2):c.559C>T(p.Arg187*) variant causes a stop gained change. The variant allele was found at a frequency of 0.00000964 in 1,452,518 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 Pathogenic (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_017813.5 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BPNT2 | NM_017813.5 | c.559C>T | p.Arg187* | stop_gained | Exon 3 of 5 | ENST00000262644.9 | NP_060283.3 | |
BPNT2 | XM_047421917.1 | c.559C>T | p.Arg187* | stop_gained | Exon 3 of 5 | XP_047277873.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BPNT2 | ENST00000262644.9 | c.559C>T | p.Arg187* | stop_gained | Exon 3 of 5 | 1 | NM_017813.5 | ENSP00000262644.4 | ||
BPNT2 | ENST00000517461.1 | c.201+2022C>T | intron_variant | Intron 2 of 2 | 5 | ENSP00000430185.1 | ||||
BPNT2 | ENST00000520392.1 | n.85C>T | non_coding_transcript_exon_variant | Exon 2 of 5 | 2 | ENSP00000428617.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000964 AC: 14AN: 1452518Hom.: 0 Cov.: 28 AF XY: 0.00000415 AC XY: 3AN XY: 723184
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Chondrodysplasia with joint dislocations, gPAPP type Pathogenic:3
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not provided Pathogenic:1
The R187X variant in the IMPAD1 gene has been reported previously in the homozygous state in two unrelated individuals with IMPAD1-related disorder (Vissers et al., 2011; Nizon et al., 2012). This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The R187X variant is not observed in large population cohorts (Lek et al., 2016). We interpret R187X as a pathogenic variant. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at