RAE1

protein-coding

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

Gene summary

Mutations in the Schizosaccharomyces pombe Rae1 and Saccharomyces cerevisiae Gle2 genes have been shown to result in accumulation of poly(A)-containing mRNA in the nucleus, suggesting that the encoded proteins are involved in RNA export. The protein encoded by this gene is a homolog of yeast Rae1. It contains four WD40 motifs, and has been shown to localize to distinct foci in the nucleoplasm, to the nuclear rim, and to meshwork-like structures throughout the cytoplasm. This gene is thought to be involved in nucleocytoplasmic transport, and in directly or indirectly attaching cytoplasmic mRNPs to the cytoskeleton. Alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

MANE transcript

NM_003610.4

Inheritance

—

ClinVar variants

U:23

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.04

Max pathogenic AF

—

Genomic locus

chr20:57,351,223-57,379,211

External References & Databases

Ensembl (ENSG00000101146)

Transcript & Mutation Effects

hg38 • Region Span ~28.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to RAE1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 31

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003610.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			22 clinvar			22
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	23	0	0	23

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 41 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003610.4	RefSeq	NP_003601.1	11	MANE Select
ENST00000395841.7	Ensembl	ENSP00000379182.2	11	MANE Select
NM_001015885.2	RefSeq	NP_001015885.1	11	Standard
ENST00000371242.6	Ensembl	ENSP00000360286.2	11	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
rae1	Danio rerio	Structure: head Quality: malformed abnormal

Gene / Model

Organism

Observed Phenotype

rae1

Danio rerio

Structure: head

Quality: malformed

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Influenza A - Homo sapiens (human)
RNA transport - Homo sapiens (human)
tRNA processing
Disease
Gene expression (Transcription)

Biological Process

transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery
mRNA export from nucleus
cell cycle
viral process
cell division

Molecular Function

RNA binding
protein binding
microtubule binding
ubiquitin binding

Cellular Component

fibrillar center
nucleus
nuclear envelope
nuclear pore
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000395841
Coding exons: 11
Length: 28202
Individuals with no LoFs: 125745
Homozygous LoFs: 0
Heterozygous LoFs: 3
Defined: 125748
p: 0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.68	100	209	0.479	0.0000108	2457
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000058	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000088	0.0000088	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.194

Intolerance Scores

LoFtool: 0.359
RVIS EVS: -0.21
RVIS percentile EVS: 38.58

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.783

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium