NM_005859.5:c.263_265delTCG

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM1PM2PM4_SupportingPP5

The NM_005859.5(PURA):​c.263_265delTCG​(p.Ile88_Ala89delinsThr) variant causes a disruptive inframe deletion change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars).

Frequency

Genomes: not found (cov: 32)

Consequence

PURA
NM_005859.5 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Pathogenic no assertion criteria provided P:1

Conservation

PhyloP100: 7.84
Variant links:
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 made for transcript

Verdict is Likely_pathogenic. Variant got 6 ACMG points.

PM1
In a hotspot region, there are 5 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 3 benign, 4 uncertain in NM_005859.5
PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in NM_005859.5. Strenght limited to Supporting due to length of the change: 1aa.
PP5
Variant 5-140114443-ATCG-A is Pathogenic according to our data. Variant chr5-140114443-ATCG-A is described in ClinVar as [Pathogenic]. Clinvar id is 156412.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
PURANM_005859.5 linkc.263_265delTCG p.Ile88_Ala89delinsThr disruptive_inframe_deletion Exon 1 of 1 ENST00000331327.5 NP_005850.1 Q00577

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
PURAENST00000331327.5 linkc.263_265delTCG p.Ile88_Ala89delinsThr disruptive_inframe_deletion Exon 1 of 1 6 NM_005859.5 ENSP00000332706.3 Q00577
PURAENST00000651386.1 linkc.263_265delTCG p.Ile88_Ala89delinsThr disruptive_inframe_deletion Exon 2 of 2 ENSP00000499133.1 Q00577
PURAENST00000505703.2 linkc.263_265delTCG p.Ile88_Ala89delinsThr disruptive_inframe_deletion Exon 2 of 2 3 ENSP00000498560.1 A0A494C0H6
PURAENST00000502351.1 linkc.*184_*186delTCG downstream_gene_variant 2 ENSP00000498760.1 A0A494C0X8

Frequencies

GnomAD3 genomes
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
Cov.:
32

ClinVar

Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link

Submissions by phenotype

Seizure;C0454644:Delayed speech and language development;C0557874:Global developmental delay;C2267233:Neonatal hypotonia;C3714756:Intellectual disability Pathogenic:1
Sep 15, 2014
Whole genome laboratory; Baylor College of Medicine
Significance: Pathogenic
Review Status: no assertion criteria provided
Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.020
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: rs587783000; hg19: chr5-139494028; API