NM_005859.5:c.697_699delTTC

Variant names:

• chr5-140114870-GCTT-G
• rs786204835
• NM_005859.5:c.697_699delTTC

Variant summary

Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM2 PM4_Supporting PP5_Very_Strong

The NM_005859.5(PURA):​c.697_699delTTC​(p.Phe233del) variant causes a conservative 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 Likely pathogenic (★★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: PURA NM_005859.5 conservative_inframe_deletion
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:15 O:1
• Conservation: PhyloP100: 8.00

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 Pathogenic. Variant got 11 ACMG points.

• 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 5-140114870-GCTT-G is Pathogenic according to our data. Variant chr5-140114870-GCTT-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 189319.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr5-140114870-GCTT-G is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PURA	NM_005859.5	c.697_699delTTC	p.Phe233del	conservative_inframe_deletion	Exon 1 of 1	ENST00000331327.5	NP_005850.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PURA	ENST00000331327.5	c.697_699delTTC	p.Phe233del	conservative_inframe_deletion	Exon 1 of 1	6	NM_005859.5	ENSP00000332706.3
PURA	ENST00000651386.1	c.697_699delTTC	p.Phe233del	conservative_inframe_deletion	Exon 2 of 2			ENSP00000499133.1

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/Likely pathogenic

Submissions summary: Pathogenic:15 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

PURA-related severe neonatal hypotonia-seizures-encephalopathy syndrome Pathogenic:9 Other:1

Feb 23, 2023

3billion

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The variant is not observed in the gnomAD v2.1.1 dataset. Inframe deletion located in a nonrepeat region was predicted to change the length of the protein and disrupt normal protein function. The variant has been previously reported as de novo in similarly affected individuals (PMID: 25342064 ‚PMID: 29150892 ‚PMID: 29097605 ‚ PMID: 28726809, PMID: 27148565). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline. -

Dec 01, 2014

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

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Clinical Genetics Department, Johns Hopkins All Children's Hospital

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

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Lifecell International Pvt. Ltd

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

A Heterozygous Inframe indel variant c.690_692delCTT in Exon 1 of the PURA gene that results in the amino acid substitution p.Phe231del was identified. The observed variant is novel in gnomAD exomes and genomes, respectively. The severity of the impact of this variant on the protein is medium, based on the effect of the protein and REVEL score . Rare Exome Variant Ensemble Learner (REVEL) is an ensembl method for predicting the pathogenicity of missense variants based on a combination of scores from 13 individual tools: MutPred, FATHMM v2.3, VEST 3.0, PolyPhen-2, SIFT, PROVEAN, MutationAssessor, MutationTaster, LRT, GERP++, SiPhy, phyloP, and phastCons. The REVEL score for an individual missense variant can range from 0 to 1, with higher scores reflecting greater likelihood that the variant is disease-causing. ClinVar has also classified this variant as Pathogenic/LikelyPathogenic (ClinVar ID: 189319). The Phe233del variant in PURA has been reported in 8 patients with autosomal dominat PURA syndrome, characterized by moderate to severe intellectual disability (ID) and several early-onset issues including motor delay, hypotonia, feeding difficulties, hyperthermia, hypersomnolence, hypoventilation/apneas, speech delay and abnormal nonepileptic movements. p.Phe233del falls in the third PUR domain that mediate dimerization, and is predicted to cause local folding defects (Reijnders MRF et al., 2018 and Hunt D et al., 2014). Based on the above evidence this variant has been classified as Pathogenic according to the ACMG guidelines. -

Oct 28, 2022

Revvity Omics, Revvity

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Apr 04, 2024

Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Jun 27, 2019

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: PURA c.697_699delTTC (p.Phe233del) results in an in-frame deletion that is predicted to remove the third Phenylalanine in a run of three Phenylalanines located in the "presumed functional domain of PURA which is necessary for homodimerisation in crystallography studies (Hunt_2014). " The variant was absent in 251468 control chromosomes (gnomAD). c.697_699delTTC has been reported in the literature in multiple individuals affected with mental retardation and delays in cognitive development (Hunt_2014, Tanaka_2015, Strauss_2017, Lee_2018, Reijnders_2018). All the patients presented the mutation as a de novo occurrence. These data indicate that the variant is very likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Three ClinVar submissions (evaluation after 2014) cite the variant as pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic. -

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GeneReviews

Significance: not provided

Review Status: no classification provided

Collection Method: literature only

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Dec 05, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant, c.697_699del, results in the deletion of 1 amino acid(s) of the PURA protein (p.Phe233del), but otherwise preserves the integrity of the reading frame. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with developmental delay, cortical visual impairment, and hypotonia (PMID: 25342064, 27148565). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 189319). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. For these reasons, this variant has been classified as Pathogenic. -

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Division of Biology and Genetics, University of Brescia

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The Phe233del variant in PURA has been reported in 8 patients with autosomal dominat PURA syndrome, characterized by moderate to severe intellectual disability (ID) and several early-onset issues including motor delay, hypotonia, feeding difficulties, hyperthermia, hypersomnolence, hypoventilation/apneas, speech delay and abnormal nonepileptic movements. Other less common manifestations include congenital heart defects, skeletal, urogenital, ophthalmological, gastrointestinal, and endocrine abnormalities; soft skin was also described as well as craniofacial dysmorphism (Reijnders et al., 1993; Hunt et al., 2014; Tanaka et al., 2015; Reijnders et al., 2018; Lee et al., 2018). p.Phe233del falls in the third PUR domain that mediate dimerization, and is predicted to cause local folding defects (Reijnders et al., 2018). Its putative pathogenicy was estimated through 3 different in silico prediction algorithms (SIFT, PROVEAN, MutPred Indel) that agreed to define p.phe233del as pathogenetic -

not provided Pathogenic:3

Mar 01, 2021

CeGaT Center for Human Genetics Tuebingen

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Oct 23, 2020

Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Mar 11, 2022

GeneDx

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

In-frame deletion of 1 amino acid in a non-repeat region; In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Not observed in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 27148565, 25342064, 29150892, 28726809, 31028937, 29097605, 31273778, 33275834) -

Inborn genetic diseases Pathogenic:1

Oct 24, 2017

Ambry Genetics

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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PURA Syndrome Pathogenic:1

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Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant has been previously reported as a de novo change in patients with intellectual disability, motor and cognitive delays hypotonia, feeding difficulties and seizures (PMID: 27148565, 31273778, 25342064). The c.697_699del (p.Phe233del) variant affects a highly conserved phenylalanine residue in the PUR repeat III which has been implicated in the dimerization of two PURA molecules (PMID: 19846792). It is absent from the gnomAD population database and thus is presumed to be rare. Analysis of the parental samples was negative for the variant, indicating this variant likely occurred as a de novo event. However, low-level parental mosaicism cannot be excluded. Based on the available evidence, the c.697_699del (p.Phe233del) variant is classified as Pathogenic. -

PURA-related disorder Pathogenic:1

Nov 08, 2023

PreventionGenetics, part of Exact Sciences

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: clinical testing

The PURA c.697_699delTTC variant is predicted to result in an in-frame deletion (p.Phe233del). This variant has been reported de novo in multiple individuals with PURA syndrome (Hunt et al. 2014. PubMed ID: 25342064; Tanaka et al. 2015. PubMed ID: 27148565; Strauss et al. 2018. PubMed ID: 28726809; Reijnders et al. 2018. PubMed ID: 29097605; Lee et al. 2018. PubMed ID: 29150892; Borlot et al. 2019. PubMed ID: 31273778; Cinquina et al. 2021. PubMed ID: 33275834). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. This variant is interpreted as pathogenic. -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs786204835; hg19: chr5-139494455;