rs793888533

chr5-140114481-TACTCTCTCC-T

Variant summary

Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2 PM4 PP3 PP5_Moderate

The NM_005859.5(PURA):c.302_310del(p.Thr101_Ser103del) variant causes a 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 (★). Synonymous variant affecting the same amino acid position (i.e. T101T) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: PURA NM_005859.5 inframe_deletion
• Clinical Significance: Pathogenic criteria provided, single submitter P:2
• Conservation: PhyloP100: 7.81

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]

ACMG classification

Verdict is Likely_pathogenic. Variant got 7 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM4: Nonframeshift variant in NON repetitive region in NM_005859.5.
• PP3: No computational evidence supports a deleterious effect, but strongly conserved according to phyloP
• PP5: Variant 5-140114481-TACTCTCTCC-T is Pathogenic according to our data. Variant chr5-140114481-TACTCTCTCC-T is described in ClinVar as [Pathogenic]. Clinvar id is 192340.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PURA	NM_005859.5	c.302_310del	p.Thr101_Ser103del	inframe_deletion	1/1	ENST00000331327.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PURA	ENST00000331327.5	c.302_310del	p.Thr101_Ser103del	inframe_deletion	1/1		NM_005859.5	P1
PURA	ENST00000505703.2	c.302_310del	p.Thr101_Ser103del	inframe_deletion	2/2	3
PURA	ENST00000651386.1	c.302_310del	p.Thr101_Ser103del	inframe_deletion	2/2			P1

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:2

Revision: criteria provided, single submitter

Submissions by phenotype

PURA-related severe neonatal hypotonia-seizures-encephalopathy syndrome Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Aug 17, 2021

- -

not provided Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

GeneDx

Feb 12, 2015

c.302_310delCTCTCTCCA: p.Thr101_Ser103del in exon 1 in the PURA gene (NM_005859.4). The normal sequence with the bases that are deleted in braces is: CTTA{CTCTCTCCA}TGTC. The c.302_310delCTCTCTCCA mutation in the PURA gene has not been reported previously as a disease-causing mutation nor as a benign polymorphism, to our knowledge. The c.302_310delCTCTCTCCA mutation was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The c.302_310delCTCTCTCCA mutation causes an in-frame deletion of three amino acids in exon 1 of the PURA gene; these amino acids are well-conserved across species. We interpret c.302_310delCTCTCTCCA as a disease-causing mutation associated with PURA-related disorders. This variant has been observed de novo with confirmed parentage. -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs793888533; hg19: chr5-139494066;