PURA

purine rich element binding protein A

Basic information

Region (hg38): 5:140107777-140125619

Links

ENSG00000185129NCBI:5813OMIM:600473HGNC:9701Uniprot:Q00577AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • PURA-related severe neonatal hypotonia-seizures-encephalopathy syndrome due to a point mutation (Supportive), mode of inheritance: AD
  • PURA-related severe neonatal hypotonia-seizures-encephalopathy syndrome due to a point mutation (Strong), mode of inheritance: AD
  • complex neurodevelopmental disorder (Definitive), mode of inheritance: AD
  • PURA-related severe neonatal hypotonia-seizures-encephalopathy syndrome due to a point mutation (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Neurodevelopmental disorder with neonatal respiratory insufficiency, hypotonia, and feeding difficultiesADGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingCraniofacial; Endocrine; Neurologic25342064; 25439098; 25533962

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PURA gene.

  • PURA-related_severe_neonatal_hypotonia-seizures-encephalopathy_syndrome (428 variants)
  • not_provided (161 variants)
  • Inborn_genetic_diseases (65 variants)
  • PURA-related_disorder (19 variants)
  • not_specified (17 variants)
  • Intellectual_disability (16 variants)
  • Global_developmental_delay (11 variants)
  • Delayed_speech_and_language_development (11 variants)
  • Neonatal_hypotonia (11 variants)
  • Seizure (9 variants)
  • PURA-related_severe_neonatal_hypotonia-seizures-encephalopathy_syndrome_due_to_a_point_mutation (7 variants)
  • PURA_Syndrome (5 variants)
  • See_cases (2 variants)
  • Neurodevelopmental_disorder (1 variants)
  • Epileptic_encephalopathy (1 variants)
  • Generalized_hypotonia (1 variants)
  • Abnormality_of_the_nervous_system (1 variants)
  • Apnea (1 variants)
  • Limb_dystonia (1 variants)
  • Global_developmental_delay-visual_anomalies-progressive_cerebellar_atrophy-truncal_hypotonia_syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PURA gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005859.5. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
1
clinvar
28
clinvar
137
clinvar
6
clinvar
172
missense
15
clinvar
47
clinvar
111
clinvar
22
clinvar
7
clinvar
202
nonsense
29
clinvar
11
clinvar
1
clinvar
41
start loss
5
2
7
frameshift
75
clinvar
28
clinvar
1
clinvar
104
splice donor/acceptor (+/-2bp)
0
Total 125 88 141 159 13

Highest pathogenic variant AF is 0.0000180341

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
PURAprotein_codingprotein_codingENST00000331327 18960
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.9400.059500000.00
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense3.37391580.2460.000007412080
Missense in Polyphen894.1510.084971065
Synonymous-3.5111072.11.530.00000344680
Loss of Function2.7708.930.003.82e-7104

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.000.00
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: This is a probable transcription activator that specifically binds the purine-rich single strand of the PUR element located upstream of the MYC gene. May play a role in the initiation of DNA replication and in recombination.;
Disease
DISEASE: Mental retardation, autosomal dominant 31 (MRD31) [MIM:616158]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. MRD31 patients manifest neonatal hypotonia, encephalopathy with or without epilepsy, and severe developmental delay. {ECO:0000269|PubMed:25342064, ECO:0000269|PubMed:25439098}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway
miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;Exercise-induced Circadian Regulation (Consensus)

Recessive Scores

pRec
0.200

Intolerance Scores

loftool
rvis_EVS
-0.12
rvis_percentile_EVS
44.54

Haploinsufficiency Scores

pHI
0.660
hipred
Y
hipred_score
0.783
ghis
0.645

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
S
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.925

Gene Damage Prediction

AllRecessiveDominant
MendelianLowLowLow
Primary ImmunodeficiencyMediumLowMedium
CancerLowLowLow

Mouse Genome Informatics

Gene name
Pura
Phenotype
nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype;

Gene ontology

Biological process
negative regulation of transcription by RNA polymerase II;DNA unwinding involved in DNA replication;DNA replication initiation;nervous system development;positive regulation of cell population proliferation;negative regulation of translation;cell differentiation;dendritic transport of messenger ribonucleoprotein complex
Cellular component
nuclear chromosome, telomeric region;nucleus;DNA replication factor A complex;dendrite cytoplasm;neuronal cell body;postsynapse;glutamatergic synapse
Molecular function
translation repressor activity, mRNA regulatory element binding;RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;double-stranded DNA binding;double-stranded telomeric DNA binding;single-stranded DNA binding;RNA binding;protein binding;transcription factor binding;purine-rich negative regulatory element binding;sequence-specific DNA binding;SMAD binding