RAI1
Basic information
Region (hg38): 17:17681458-17811453
Previous symbols: [ "SMCR" ]
Links
Phenotypes
GenCC
Source:
- Smith-Magenis syndrome (Definitive), mode of inheritance: AD
- Smith-Magenis syndrome (Supportive), mode of inheritance: AD
- Potocki-Lupski syndrome (Moderate), mode of inheritance: AD
- Smith-Magenis syndrome (Definitive), mode of inheritance: AD
- Smith-Magenis syndrome (Strong), mode of inheritance: AD
- Smith-Magenis syndrome (Definitive), mode of inheritance: AD
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Smith-Magenis syndrome | AD | Neurologic | The condition may involve sleep disturbances, and treatment with specific agents (eg, tasimelteon) may be beneficial | Craniofacial; Musculoskeletal; Neurologic; Ophthalmologic | 12652298; 15788730; 16845274; 17539903; 21739587; 21897445; 22578325; 34316024 |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (49 variants)
- Smith-Magenis syndrome (14 variants)
- Inborn genetic diseases (8 variants)
- Intellectual disability (3 variants)
- RAI1-related disorder (1 variants)
- Developmental disorder (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAI1 gene is commonly pathogenic or not.
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.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 534 | 17 | 560 | |||
missense | 690 | 144 | 100 | 937 | ||
nonsense | 21 | 27 | ||||
start loss | 0 | |||||
frameshift | 51 | 18 | 75 | |||
inframe indel | 29 | 26 | 58 | |||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 1 | 2 | 2 | 1 | 6 | |
non coding | 23 | 34 | ||||
Total | 73 | 27 | 730 | 729 | 132 |
Highest pathogenic variant AF is 0.00000657
Variants in RAI1
This is a list of pathogenic ClinVar variants found in the RAI1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
RAI1 | protein_coding | protein_coding | ENST00000353383 | 4 | 129981 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
1.00 | 7.14e-8 | 125693 | 0 | 5 | 125698 | 0.0000199 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.12 | 1029 | 1.13e+3 | 0.907 | 0.0000747 | 12193 |
Missense in Polyphen | 227 | 323.88 | 0.70087 | 3566 | ||
Synonymous | -3.04 | 610 | 522 | 1.17 | 0.0000376 | 4106 |
Loss of Function | 6.58 | 2 | 54.4 | 0.0368 | 0.00000306 | 629 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.0000677 | 0.0000616 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.0000555 | 0.0000544 |
Finnish | 0.0000465 | 0.0000462 |
European (Non-Finnish) | 0.0000178 | 0.0000176 |
Middle Eastern | 0.0000555 | 0.0000544 |
South Asian | 0.00 | 0.00 |
Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcriptional regulator of the circadian clock components: CLOCK, ARNTL/BMAL1, ARNTL2/BMAL2, PER1/3, CRY1/2, NR1D1/2 and RORA/C. Positively regulates the transcriptional activity of CLOCK a core component of the circadian clock. Regulates transcription through chromatin remodeling by interacting with other proteins in chromatin as well as proteins in the basic transcriptional machinery. May be important for embryonic and postnatal development. May be involved in neuronal differentiation. {ECO:0000269|PubMed:22578325}.;
- Disease
- DISEASE: Smith-Magenis syndrome (SMS) [MIM:182290]: Characterized by congenital mental retardation associated with development and growth delays. Affected persons have characteristic behavioral abnormalities, including self-injurious behaviors and sleep disturbance, and distinct craniofacial and skeletal anomalies. {ECO:0000269|PubMed:11404004, ECO:0000269|PubMed:12652298, ECO:0000269|PubMed:24863970}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.117
Intolerance Scores
- loftool
- 0.202
- rvis_EVS
- -3.68
- rvis_percentile_EVS
- 0.25
Haploinsufficiency Scores
- pHI
- 0.137
- hipred
- Y
- hipred_score
- 0.572
- ghis
- 0.668
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.753
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rai1
- Phenotype
- homeostasis/metabolism phenotype; craniofacial phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; growth/size/body region phenotype; respiratory system phenotype; skeleton phenotype; limbs/digits/tail 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); normal 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan);
Gene ontology
- Biological process
- skeletal system development;circadian regulation of gene expression;negative regulation of multicellular organism growth;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II
- Cellular component
- nucleus;nucleoplasm;mitochondrion
- Molecular function
- DNA-binding transcription factor activity;protein binding;enhancer binding;transcription regulatory region DNA binding;metal ion binding