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

Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000096 ( 0 hom. )

Consequence

BPNT2
NM_017813.5 stop_gained

Scores

4
2
1

Clinical Significance

Pathogenic criteria provided, multiple submitters, no conflicts P:4

Conservation

PhyloP100: 4.16
Variant links:
Genes affected
BPNT2 (HGNC:26019): (3'(2'), 5'-bisphosphate nucleotidase 2) This gene encodes a member of the inositol monophosphatase family. The encoded protein is localized to the Golgi apparatus and catalyzes the hydrolysis of phosphoadenosine phosphate (PAP) to adenosine monophosphate (AMP). Mutations in this gene are a cause of GRAPP type chondrodysplasia with joint dislocations, and a pseudogene of this gene is located on the long arm of chromosome 1. [provided by RefSeq, Dec 2011]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 18 ACMG points.

PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 8-56978137-G-A is Pathogenic according to our data. Variant chr8-56978137-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 31092.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
BPNT2NM_017813.5 linkc.559C>T p.Arg187* stop_gained Exon 3 of 5 ENST00000262644.9 NP_060283.3 Q9NX62A0A024R7W0
BPNT2XM_047421917.1 linkc.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
BPNT2ENST00000262644.9 linkc.559C>T p.Arg187* stop_gained Exon 3 of 5 1 NM_017813.5 ENSP00000262644.4 Q9NX62
BPNT2ENST00000517461.1 linkc.201+2022C>T intron_variant Intron 2 of 2 5 ENSP00000430185.1 H0YBS3
BPNT2ENST00000520392.1 linkn.85C>T non_coding_transcript_exon_variant Exon 2 of 5 2 ENSP00000428617.1 H0YB38

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
AF:
0.00000964
AC:
14
AN:
1452518
Hom.:
0
Cov.:
28
AF XY:
0.00000415
AC XY:
3
AN XY:
723184
show subpopulations
Gnomad4 AFR exome
AF:
0.0000300
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000118
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32
Alfa
AF:
0.0000308
Hom.:
0

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

Chondrodysplasia with joint dislocations, gPAPP type Pathogenic:3
Oct 23, 2022
Baylor Genetics
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Sep 01, 2012
OMIM
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: literature only

- -

Jul 29, 2019
Knight Diagnostic Laboratories, Oregon Health and Sciences University
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

not provided Pathogenic:1
Nov 30, 2017
GeneDx
Significance: Pathogenic
Review Status: criteria provided, single submitter
Collection Method: clinical testing

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: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
0.63
D
BayesDel_noAF
Pathogenic
0.62
CADD
Pathogenic
46
DANN
Uncertain
1.0
Eigen
Pathogenic
1.1
Eigen_PC
Pathogenic
0.94
FATHMM_MKL
Uncertain
0.93
D
Vest4
0.38
GERP RS
6.0

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs387907103; hg19: chr8-57890696; COSMIC: COSV52906942; API