PURA
Basic information
Region (hg38): 5:140107777-140125619
Links
Phenotypes
GenCC
Source:
- 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:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Neurodevelopmental disorder with neonatal respiratory insufficiency, hypotonia, and feeding difficulties | AD | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Craniofacial; Endocrine; Neurologic | 25342064; 25439098; 25533962 |
ClinVar
This is a list of variants' phenotypes submitted to
- 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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 28 | 137 | 172 | |||
missense | 15 | 47 | 111 | 22 | 202 | |
nonsense | 29 | 11 | 41 | |||
start loss | 5 | 2 | 7 | |||
frameshift | 75 | 28 | 104 | |||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 125 | 88 | 141 | 159 | 13 |
Highest pathogenic variant AF is 0.0000180341
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
PURA | protein_coding | protein_coding | ENST00000331327 | 1 | 8960 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.940 | 0.0595 | 0 | 0 | 0 | 0 | 0.00 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 3.37 | 39 | 158 | 0.246 | 0.00000741 | 2080 |
Missense in Polyphen | 8 | 94.151 | 0.08497 | 1065 | ||
Synonymous | -3.51 | 110 | 72.1 | 1.53 | 0.00000344 | 680 |
Loss of Function | 2.77 | 0 | 8.93 | 0.00 | 3.82e-7 | 104 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00 | 0.00 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.00 | 0.00 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Low | Low | Low |
Primary Immunodeficiency | Medium | Low | Medium |
Cancer | Low | Low | Low |
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