chr5-140114481-TACTCTCTCC-T

Variant names:

• chr5-140114481-TACTCTCTCC-T
• rs793888533
• NM_005859.5:c.302_310delCTCTCTCCA

Variant summary

Our verdict is Likely pathogenic. The variant received 9 ACMG points: 9P and 0B. PM1 PM2 PM4 PP3 PP5_Moderate

The NM_005859.5(PURA):​c.302_310delCTCTCTCCA​(p.Thr101_Ser103del) 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 (★). 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 disruptive_inframe_deletion
• Clinical Significance: Pathogenic criteria provided, single submitter P:2
• Conservation: PhyloP100: 7.81
• Publications: 3 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]

MALINC1 (HGNC:49009): (mitosis associated long intergenic non-coding RNA 1)

ACMG classification

Our verdict: Likely_pathogenic. The variant received 9 ACMG points.

• PM1: In a hotspot region, there are 5 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 2 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.
• 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 VariationId is 192340.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.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PURA	NM_005859.5	MANE Select	c.302_310delCTCTCTCCA	p.Thr101_Ser103del	disruptive_inframe_deletion	Exon 1 of 1	NP_005850.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PURA	ENST00000331327.5	TSL:6 MANE Select	c.302_310delCTCTCTCCA	p.Thr101_Ser103del	disruptive_inframe_deletion	Exon 1 of 1	ENSP00000332706.3
	PURA	ENST00000651386.1		c.302_310delCTCTCTCCA	p.Thr101_Ser103del	disruptive_inframe_deletion	Exon 2 of 2	ENSP00000499133.1
	PURA	ENST00000505703.2	TSL:3	c.302_310delCTCTCTCCA	p.Thr101_Ser103del	disruptive_inframe_deletion	Exon 2 of 2	ENSP00000498560.1

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

Aug 17, 2021

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

not provided Pathogenic:1

Feb 12, 2015

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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 v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		7.8
Mutation Taster		=2/198	disease causing (ClinVar)

Splicing

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

Other links and lift over

dbSNP: rs793888533; hg19: chr5-139494066;