RAE1

ribonucleic acid export 1, the group of WD repeat domain containing|Nucleoporins

Basic information

Region (hg38): 20:57351223-57379211

Links

ENSG00000101146 ∙ NCBI:8480 ∙ OMIM:603343 ∙ HGNC:9828 ∙ Uniprot:P78406 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 20.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
ENST00000371242.6	ENSP00000360286.2	11	-	-
ENST00000395840.6	ENSP00000379181.2	11	-	-
ENST00000395841.7	ENSP00000379182.2	11	yes	-
ENST00000411894.5	ENSP00000392097.1	5	-	-

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the RAE1 gene.

• not_specified (30 variants)
• not_provided (2 variants)

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. These statistics are base on transcript: NM_000003610.4. 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	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			21			21
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	21	0	0

GnomAD

Source: gnomAD

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
		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: dbNSFP

• 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

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

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