RAE1
ribonucleic acid export 1, the group of WD repeat domain containing|Nucleoporins
Basic information
Region (hg38): 20:57351223-57379211
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RAE1 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 | 0 | |||||
| missense | 12 | 12 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 8 | |||||
| Total | 0 | 0 | 20 | 0 | 0 |
Variants in RAE1
This is a list of pathogenic ClinVar variants found in the RAE1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 20-57354112-A-G | not specified | Uncertain significance (Aug 12, 2021) | ||
| 20-57354704-T-G | Benign (Jul 06, 2018) | |||
| 20-57354715-A-G | not specified | Uncertain significance (Oct 03, 2022) | ||
| 20-57354731-C-G | not specified | Uncertain significance (Jan 23, 2023) | ||
| 20-57358972-C-T | not specified | Uncertain significance (Jan 26, 2022) | ||
| 20-57358973-G-A | not specified | Uncertain significance (Feb 06, 2025) | ||
| 20-57358982-C-T | not specified | Uncertain significance (Jan 10, 2023) | ||
| 20-57358991-C-G | not specified | Uncertain significance (Feb 06, 2024) | ||
| 20-57358993-A-G | not specified | Uncertain significance (May 09, 2023) | ||
| 20-57358993-A-T | not specified | Uncertain significance (Mar 07, 2023) | ||
| 20-57359017-C-T | not specified | Uncertain significance (Dec 22, 2023) | ||
| 20-57359035-G-T | not specified | Uncertain significance (Sep 09, 2024) | ||
| 20-57359036-C-T | not specified | Uncertain significance (Sep 09, 2024) | ||
| 20-57365430-A-G | not specified | Uncertain significance (Mar 28, 2024) | ||
| 20-57366828-A-G | not specified | Uncertain significance (Oct 16, 2023) | ||
| 20-57366839-C-G | Uncertain significance (-) | |||
| 20-57367041-G-A | not specified | Uncertain significance (Nov 07, 2024) | ||
| 20-57367077-G-A | not specified | Uncertain significance (Feb 28, 2024) | ||
| 20-57368705-A-G | not specified | Uncertain significance (Dec 02, 2022) | ||
| 20-57373569-A-G | not specified | Uncertain significance (Nov 11, 2024) | ||
| 20-57374724-G-C | not specified | Uncertain significance (Apr 15, 2024) | ||
| 20-57378026-A-G | not specified | Uncertain significance (Apr 19, 2023) | ||
| 20-57378037-A-G | not specified | Uncertain significance (Nov 26, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RAE1 | protein_coding | protein_coding | ENST00000395841 | 11 | 28202 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.999 | 0.000979 | 125745 | 0 | 3 | 125748 | 0.0000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.68 | 100 | 209 | 0.479 | 0.0000108 | 2457 |
| Missense in Polyphen | 15 | 58.64 | 0.2558 | 709 | ||
| Synonymous | -0.518 | 79 | 73.4 | 1.08 | 0.00000444 | 660 |
| Loss of Function | 4.40 | 1 | 24.5 | 0.0408 | 0.00000137 | 251 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000579 | 0.0000579 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000879 | 0.00000879 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Plays a role in mitotic bipolar spindle formation (PubMed:17172455). Binds mRNA. May function in nucleocytoplasmic transport and in directly or indirectly attaching cytoplasmic mRNPs to the cytoskeleton. {ECO:0000269|PubMed:17172455}.;
- Pathway
- Influenza A - Homo sapiens (human);RNA transport - Homo sapiens (human);tRNA processing;Disease;Gene expression (Transcription);Regulation of HSF1-mediated heat shock response;Metabolism of carbohydrates;Rev-mediated nuclear export of HIV RNA;Late Phase of HIV Life Cycle;HIV Life Cycle;Interactions of Rev with host cellular proteins;Host Interactions of HIV factors;HIV Infection;snRNP Assembly;Vpr-mediated nuclear import of PICs;SUMOylation of DNA damage response and repair proteins;Transport of Ribonucleoproteins into the Host Nucleus;Viral Messenger RNA Synthesis;Export of Viral Ribonucleoproteins from Nucleus;SUMOylation of chromatin organization proteins;Influenza Viral RNA Transcription and Replication;Cellular responses to stress;SUMOylation of RNA binding proteins;Post-translational protein modification;SUMOylation of DNA replication proteins;SUMO E3 ligases SUMOylate target proteins;NEP/NS2 Interacts with the Cellular Export Machinery;Metabolism of proteins;Influenza Life Cycle;Influenza Infection;Metabolism of RNA;Infectious disease;Metabolism;Transport of the SLBP independent Mature mRNA;Transport of the SLBP Dependant Mature mRNA;Transport of Mature mRNA Derived from an Intronless Transcript;Transport of Mature mRNAs Derived from Intronless Transcripts;SUMOylation;Cellular responses to external stimuli;Regulation of Glucokinase by Glucokinase Regulatory Protein;Glycolysis;Nuclear Pore Complex (NPC) Disassembly;tRNA processing in the nucleus;Transport of Mature mRNA derived from an Intron-Containing Transcript;Metabolism of non-coding RNA;Cellular response to heat stress;Nuclear Envelope Breakdown;Mitotic Prophase;M Phase;Nuclear import of Rev protein;Glucose metabolism;Transcriptional regulation by small RNAs;Cell Cycle;Interactions of Vpr with host cellular proteins;Cell Cycle, Mitotic;Transport of Mature Transcript to Cytoplasm;Processing of Capped Intron-Containing Pre-mRNA;Gene Silencing by RNA
(Consensus)
Recessive Scores
- pRec
- 0.194
Intolerance Scores
- loftool
- 0.359
- rvis_EVS
- -0.21
- rvis_percentile_EVS
- 38.58
Haploinsufficiency Scores
- pHI
- 0.497
- hipred
- Y
- hipred_score
- 0.802
- ghis
- 0.628
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.783
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rae1
- Phenotype
- neoplasm; 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); embryo phenotype; skeleton phenotype; vision/eye phenotype; muscle phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype;
Zebrafish Information Network
- Gene name
- rae1
- Affected structure
- head
- Phenotype tag
- abnormal
- Phenotype quality
- malformed
Gene ontology
- Biological process
- transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery;mRNA export from nucleus;cell cycle;viral process;cell division;regulation of mitotic spindle organization;cellular response to organic cyclic compound
- Cellular component
- fibrillar center;nucleus;nuclear envelope;nuclear pore;cytoplasm;mitotic spindle pole
- Molecular function
- RNA binding;protein binding;microtubule binding;ubiquitin binding