NM_005859.5:c.159delG
Variant names:
Variant summary
Our verdict is Pathogenic. The variant received 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_005859.5(PURA):c.159delG(p.Leu54CysfsTer24) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
PURA
NM_005859.5 frameshift
NM_005859.5 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.70
Publications
2 publications found
Genes affected
PURA (HGNC:9701): (purine rich element binding protein A) This gene product is a sequence-specific, single-stranded DNA-binding protein. It binds preferentially to the single strand of the purine-rich element termed PUR, which is present at origins of replication and in gene flanking regions in a variety of eukaryotes from yeasts through humans. Thus, it is implicated in the control of both DNA replication and transcription. Deletion of this gene has been associated with myelodysplastic syndrome and acute myelogenous leukemia. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification was made for transcript
Our verdict: Pathogenic. The variant received 12 ACMG points.
PVS1
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. There are 173 pathogenic variants in the truncated region.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 5-140114334-AG-A is Pathogenic according to our data. Variant chr5-140114334-AG-A is described in ClinVar as Pathogenic. ClinVar VariationId is 2664962.Status of the report is criteria_provided_single_submitter, 1 stars.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_005859.5. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| PURA | TSL:6 MANE Select | c.159delG | p.Leu54CysfsTer24 | frameshift | Exon 1 of 1 | ENSP00000332706.3 | Q00577 | ||
| PURA | c.159delG | p.Leu54CysfsTer24 | frameshift | Exon 2 of 2 | ENSP00000499133.1 | Q00577 | |||
| PURA | TSL:3 | c.159delG | p.Leu54CysfsTer24 | frameshift | Exon 2 of 2 | ENSP00000498560.1 | A0A494C0H6 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 1287560Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 636982
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
AC:
0
AN:
1287560
Hom.:
Cov.:
33
AF XY:
AC XY:
0
AN XY:
636982
African (AFR)
AF:
AC:
0
AN:
27480
American (AMR)
AF:
AC:
0
AN:
28324
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
21382
East Asian (EAS)
AF:
AC:
0
AN:
30124
South Asian (SAS)
AF:
AC:
0
AN:
62320
European-Finnish (FIN)
AF:
AC:
0
AN:
31616
Middle Eastern (MID)
AF:
AC:
0
AN:
4428
European-Non Finnish (NFE)
AF:
AC:
0
AN:
1029580
Other (OTH)
AF:
AC:
0
AN:
52306
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
ClinVar submissions
View on ClinVar Significance:Pathogenic
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
1
-
-
PURA-related severe neonatal hypotonia-seizures-encephalopathy syndrome (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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