RASEF

gene
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Also known as FLJ31614TSG

Summary

RASEF (RAS and EF-hand domain containing, HGNC:26464) is a protein-coding gene on chromosome 9q21.32, encoding Ras and EF-hand domain-containing protein (Q8IZ41). Rab GTPase that acts as a dynein adapter protein, thereby activating dynein-mediated transport and dynein-dynactin motility on microtubules.

This gene is a member of the Rab family of GTPases that are involved in regulation of membrane traffic. The encoded protein contains an N-terminal EF-hand domain, a coiled-coil motif and a C-terminal Rab domain. A potential role as tumor suppressor has been indicated for this gene.

Source: NCBI Gene 158158 — RefSeq curated summary.

At a glance

  • GWAS associations: 9
  • Clinical variants (ClinVar): 151 total
  • MANE Select transcript: NM_152573

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:26464
Approved symbolRASEF
NameRAS and EF-hand domain containing
Location9q21.32
Locus typegene with protein product
StatusApproved
AliasesFLJ31614, TSG
Ensembl geneENSG00000165105
Ensembl biotypeprotein_coding
OMIM611344
Entrez158158

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 7 protein_coding

ENST00000340717, ENST00000376447, ENST00000873431, ENST00000873432, ENST00000873433, ENST00000873434, ENST00000928035

RefSeq mRNA: 1 — MANE Select: NM_152573 NM_152573

CCDS: CCDS6662

Canonical transcript exons

ENST00000376447 — 17 exons

ExonStartEnd
ENSE000010904228301243483012511
ENSE000010904258301580583015900
ENSE000010904288302233683022426
ENSE000010904328300964183009756
ENSE000012933628300743783007505
ENSE000012941948300089683001130
ENSE000012958358297959082982782
ENSE000012987978300016983000316
ENSE000012998078299290682993025
ENSE000013077938302577583025921
ENSE000013080488300541683005500
ENSE000013137708300043383000570
ENSE000013170278299039182990467
ENSE000013210828299701282997126
ENSE000013287638300449883004586
ENSE000013835548299836582998446
ENSE000013912508306243783063142

Expression profiles

Bgee: expression breadth ubiquitous, 182 present calls, max score 98.03.

FANTOM5 (CAGE): breadth broad, TPM avg 2.0821 / max 100.1381, expressed in 427 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
1011281.2907329
1011270.3472161
1011250.1930123
2055340.157885
1011260.093650

Top tissues by expression

242 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
epithelial cell of pancreasCL:000008398.03gold quality
ileal mucosaUBERON:000033194.63gold quality
spermCL:000001993.48gold quality
mucosa of sigmoid colonUBERON:000499392.72gold quality
colonic mucosaUBERON:000031791.65gold quality
oviduct epitheliumUBERON:000480490.48gold quality
pancreatic ductal cellCL:000207990.42gold quality
caput epididymisUBERON:000435890.07gold quality
esophagus squamous epitheliumUBERON:000692089.16gold quality
epithelium of nasopharynxUBERON:000195188.90gold quality
secondary oocyteCL:000065588.82gold quality
bronchial epithelial cellCL:000232888.74gold quality
bronchusUBERON:000218588.59gold quality
body of pancreasUBERON:000115088.45gold quality
nasal cavity epitheliumUBERON:000538487.94gold quality
tracheaUBERON:000312687.39gold quality
palpebral conjunctivaUBERON:000181287.36gold quality
amniotic fluidUBERON:000017387.17gold quality
corpus epididymisUBERON:000435986.64gold quality
pancreasUBERON:000126486.54gold quality
nasal cavity mucosaUBERON:000182685.23gold quality
rectumUBERON:000105285.00gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047384.10gold quality
parotid glandUBERON:000183183.92gold quality
oocyteCL:000002383.86gold quality
pharyngeal mucosaUBERON:000035583.59gold quality
pylorusUBERON:000116683.57gold quality
islet of LangerhansUBERON:000000683.36gold quality
epithelium of mammary glandUBERON:000324483.26gold quality
mammary ductUBERON:000176583.12gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 3.

ExperimentMarker?Max mean expression
E-MTAB-10018yes1105.93
E-ANND-3yes13.09
E-MTAB-7249yes11.13
E-MTAB-4850no5.38

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

155 targeting RASEF, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-5692A100.0074.406850
HSA-MIR-1277-5P100.0073.955056
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-126-5P100.0072.713180
HSA-MIR-3646100.0073.565283
HSA-MIR-4262100.0073.263931
HSA-MIR-513A-5P100.0069.772465
HSA-MIR-3163100.0077.238605
HSA-MIR-340-5P100.0072.504437
HSA-MIR-8485100.0077.574731
HSA-MIR-4747-5P100.0067.902681
HSA-MIR-5196-5P100.0067.982761
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-33A-5P99.9968.621055
HSA-MIR-33B-5P99.9968.581062
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-181A-5P99.9972.962995
HSA-MIR-181B-5P99.9972.972996
HSA-MIR-181C-5P99.9972.952996
HSA-MIR-181D-5P99.9973.042997
HSA-MIR-223-3P99.9970.141140
HSA-MIR-3692-3P99.9870.272139
HSA-MIR-548N99.9871.944170
HSA-LET-7F-2-3P99.9870.982588
HSA-MIR-1185-1-3P99.9871.042593
HSA-MIR-1185-2-3P99.9871.042593
HSA-MIR-4789-5P99.9870.762721

Literature-anchored findings (GeneRIF, showing 3)

  • Homozygosity, in combination with methylation, appears to be the mechanism targeting RASEF in uveal melanoma, and allelic imbalance at this locus supports a TSG role for RASEF. (PMID:18385040)
  • overexpression of RAB45 increased the phosphorylation levels of p38, resulting in the induction of apoptosis and inhibition of proliferation of CML progenitor cells (PMID:21890458)
  • Near-genomewide RNAi screening for regulators of BRAF(V600E) -induced senescence identifies RASEF, a gene epigenetically silenced in melanoma. (PMID:24703243)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_reriorasefENSDARG00000076250
mus_musculusRasefENSMUSG00000043003
rattus_norvegicusRasefENSRNOG00000024190

Paralogs (68): RAB27B (ENSG00000041353), RAB27A (ENSG00000069974), RAB7A (ENSG00000075785), RABL2B (ENSG00000079974), RAB21 (ENSG00000080371), RAB10 (ENSG00000084733), RAB18 (ENSG00000099246), RAB36 (ENSG00000100228), IFT27 (ENSG00000100360), RAB40AL (ENSG00000102128), RAB11A (ENSG00000103769), RAB2A (ENSG00000104388), RAB3D (ENSG00000105514), RAB3A (ENSG00000105649), RAB5C (ENSG00000108774), RAB34 (ENSG00000109113), RAB5B (ENSG00000111540), RAB35 (ENSG00000111737), RAB23 (ENSG00000112210), DNAJC27 (ENSG00000115137), RAB29 (ENSG00000117280), RAB32 (ENSG00000118508), RAB14 (ENSG00000119396), RAB9B (ENSG00000123570), RAB9A (ENSG00000123595), RAB38 (ENSG00000123892), RAB22A (ENSG00000124209), RAB17 (ENSG00000124839), RAB2B (ENSG00000129472), RAB25 (ENSG00000132698), RAB33A (ENSG00000134594), RAB30 (ENSG00000137502), RAB1A (ENSG00000138069), RAB20 (ENSG00000139832), RAB15 (ENSG00000139998), RAB40B (ENSG00000141542), RAB13 (ENSG00000143545), RABL2A (ENSG00000144134), RAB5A (ENSG00000144566), RAB19 (ENSG00000146955)

Protein

Protein identifiers

Ras and EF-hand domain-containing proteinQ8IZ41 (reviewed: Q8IZ41)

Alternative names: Ras-related protein Rab-45

All UniProt accessions (1): Q8IZ41

UniProt curated annotations — full annotation on UniProt →

Function. Rab GTPase that acts as a dynein adapter protein, thereby activating dynein-mediated transport and dynein-dynactin motility on microtubules. RASEF-mediated dynein motility is Ca(2+)-independent. Also regulates the formation and sorting of zymogen granules and secretion of digestive enzymes by pancreatic acinar cells.

Subunit / interactions. Homodimer. Interacts with the dynein-dynactin complex.

Subcellular location. Cytoplasm. Perinuclear region. Golgi apparatus. Early endosome. Late endosome. Lysosome.

Tissue specificity. Down-regulated in cutaneous melanoma cells but not in breast cancer cells.

Similarity. Belongs to the small GTPase superfamily. Rab family.

Isoforms (2)

UniProt IDNamesCanonical?
Q8IZ41-11yes
Q8IZ41-22

RefSeq proteins (1): NP_689786* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001806Small_GTPaseFamily
IPR002048EF_hand_domDomain
IPR005225Small_GTP-bdDomain
IPR011992EF-hand-dom_pairHomologous_superfamily
IPR018247EF_Hand_1_Ca_BSBinding_site
IPR027417P-loop_NTPaseHomologous_superfamily
IPR050227RabFamily

Pfam: PF00071, PF13499

Catalyzed reactions (Rhea), 1 shown:

  • GTP + H2O = GDP + phosphate + H(+) (RHEA:19669)

UniProt features (77 total): binding site 36, helix 13, strand 8, region of interest 5, compositionally biased region 3, domain 2, modified residue 2, splice variant 2, mutagenesis site 2, chain 1, sequence variant 1, turn 1, coiled-coil region 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
2P5SX-RAY DIFFRACTION2.15
2PMYX-RAY DIFFRACTION2.3

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8IZ41-F170.910.29

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (36): 21; 23; 25; 27; 29; 32; 55; 57; 59; 61; 66; 551

Post-translational modifications (2): 377, 383

Mutagenesis-validated functional residues (2):

PositionPhenotype
555impairs nucleotide binding and perinuclear localization.
600favors gtp association.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 113 (showing top): PEREZ_TP63_TARGETS, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_EXOCYTOSIS, BILD_E2F3_ONCOGENIC_SIGNATURE, GOBP_SECRETION, PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_UP, TGANTCA_AP1_C, GOBP_CALCIUM_ION_REGULATED_EXOCYTOSIS, PEREZ_TP53_AND_TP63_TARGETS, TGGAAA_NFAT_Q4_01, GOCC_ENDOLYSOSOME, CHARAFE_BREAST_CANCER_LUMINAL_VS_MESENCHYMAL_UP, chr9q21, GOMF_GTPASE_ACTIVITY, GOMF_GDP_BINDING

GO Biological Process (2): vesicle-mediated transport (GO:0016192), zymogen granule exocytosis (GO:0070625)

GO Molecular Function (8): GTPase activity (GO:0003924), G protein activity (GO:0003925), calcium ion binding (GO:0005509), GTP binding (GO:0005525), GDP binding (GO:0019003), identical protein binding (GO:0042802), nucleotide binding (GO:0000166), metal ion binding (GO:0046872)

GO Cellular Component (6): cytoplasm (GO:0005737), early endosome (GO:0005769), Golgi apparatus (GO:0005794), cytosol (GO:0005829), endolysosome (GO:0036019), perinuclear region of cytoplasm (GO:0048471)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
cytoplasm3
guanyl ribonucleotide binding2
endosome2
transport1
cellular process1
calcium-ion regulated exocytosis1
ribonucleoside triphosphate phosphatase activity1
GTPase activity1
molecular function regulator activity1
metal ion binding1
purine ribonucleoside triphosphate binding1
anion binding1
protein binding1
nucleoside phosphate binding1
heterocyclic compound binding1
cation binding1
intracellular anatomical structure1
endomembrane system1
intracellular membrane-bounded organelle1
lysosome1

Protein interactions and networks

STRING

808 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
RASEFFRMD3A2A2Y4622
RASEFBICDL1Q6ZP65526
RASEFRAB11FIP3O75154497
RASEFCD34P28906496
RASEFTMEM210A6NLX4493
RASEFTLE1Q04724476
RASEFTLE4Q04727469
RASEFBICDL2A1A5D9460
RASEFSMIM9A6NGZ8450
RASEFACP3P15309445
RASEFGNAQP50148444
RASEFPSAT1Q9Y617437
RASEFOR5H2Q8NGV7432
RASEFNPAP1Q9NZP6424
RASEFTTC9Q92623420

IntAct

28 interactions, top by confidence:

ABTypeScore
GDI1RAB4Apsi-mi:“MI:0914”(association)0.820
CFTRESYT2psi-mi:“MI:0914”(association)0.710
FAM9CNDC80psi-mi:“MI:0914”(association)0.670
CFTRRASEFpsi-mi:“MI:0403”(colocalization)0.580
PPFIBP2SNAP29psi-mi:“MI:0914”(association)0.530
CFTRPLEKHG3psi-mi:“MI:0914”(association)0.480
RABL2BRASEFpsi-mi:“MI:0914”(association)0.350
CFTRMYH7Bpsi-mi:“MI:0914”(association)0.350
MAPRE1SCAMP1psi-mi:“MI:0914”(association)0.350
RASEFBLTP3Bpsi-mi:“MI:0914”(association)0.350
GDI1NADKpsi-mi:“MI:0914”(association)0.350
RABL2BCEP43psi-mi:“MI:0914”(association)0.350
SLC22A11CNOT1psi-mi:“MI:0914”(association)0.350
ATF6psi-mi:“MI:2364”(proximity)0.270

BioGRID (51): RASEF (Affinity Capture-MS), RASEF (Affinity Capture-MS), RASEF (Affinity Capture-MS), RASEF (Affinity Capture-RNA), RASEF (Affinity Capture-MS), RASEF (Proximity Label-MS), RASEF (Negative Genetic), RASEF (Proximity Label-MS), RASEF (Proximity Label-MS), RASEF (Proximity Label-MS), SRC (Affinity Capture-MS), UHRF1BP1 (Affinity Capture-MS), UHRF1BP1L (Affinity Capture-MS), ITPR3 (Affinity Capture-MS), DYNC1LI2 (Affinity Capture-MS)

ESM2 similar proteins: A0A072VIM5, A0A0K0PU92, A2CIR7, F4IG73, F4JD14, G3LSH3, G8GTN7, O23052, O42132, O80560, P03372, P0CI65, P19785, P48423, P50242, P57717, P57753, Q0JJ01, Q29040, Q2HW56, Q2QXZ2, Q2RAQ5, Q337A0, Q53AD2, Q5D0W8, Q5YLM1, Q5ZLG9, Q69ZR2, Q6KAE5, Q6NLQ8, Q6PJI9, Q6WQJ1, Q7EZ44, Q7Z494, Q8C0M0, Q8CFE5, Q8IPH9, Q8IZ41, Q9CAJ9, Q9FDY4

Diamond homologs: A4FV54, A5WW21, C4YL11, F1PTE3, O24466, O42819, P07560, P0CY30, P0CY31, P10536, P11620, P16976, P17609, P17610, P20790, P20791, P22125, P22127, P22128, P24409, P28186, P28187, P28188, P31584, P33723, P34139, P34140, P35280, P35286, P36861, P40392, P40393, P41924, P51153, P51156, P55258, P61006, P61007, P61019, P61026

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

151 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance110
Likely benign6
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

3212 predictions. Top by Δscore:

VariantEffectΔscore
9:82997127:C:CCacceptor_gain1.0000
9:83000894:A:ACdonor_gain1.0000
9:83000895:C:CCdonor_gain1.0000
9:83000895:CAT:Cdonor_gain1.0000
9:83000917:T:TAdonor_gain1.0000
9:83000927:T:Adonor_gain1.0000
9:83000988:A:ACdonor_gain1.0000
9:83000989:C:CCdonor_gain1.0000
9:83000992:A:ACdonor_gain1.0000
9:83001127:TGAC:Tacceptor_gain1.0000
9:83001128:GACCT:Gacceptor_loss1.0000
9:83001129:ACCTG:Aacceptor_loss1.0000
9:83001131:C:CCacceptor_gain1.0000
9:83001132:T:Aacceptor_loss1.0000
9:83003625:TAA:Tdonor_gain1.0000
9:83003626:AAA:Adonor_gain1.0000
9:83004583:TATG:Tacceptor_gain1.0000
9:83004585:TG:Tacceptor_gain1.0000
9:83004587:C:CCacceptor_gain1.0000
9:83009756:CCTGG:Cacceptor_loss1.0000
9:83009757:C:Aacceptor_loss1.0000
9:83009757:C:CCacceptor_gain1.0000
9:83009758:T:Aacceptor_loss1.0000
9:83012508:CGAG:Cacceptor_gain1.0000
9:83015813:G:Cdonor_gain1.0000
9:83015896:TTTTC:Tacceptor_gain1.0000
9:83015897:TTTC:Tacceptor_gain1.0000
9:83015898:TTC:Tacceptor_gain1.0000
9:83015899:TC:Tacceptor_gain1.0000
9:83015899:TCCT:Tacceptor_loss1.0000

AlphaMissense

4893 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
9:82998383:T:GD596A0.999
9:82990397:A:GL704P0.998
9:82997123:G:CF603L0.998
9:82997123:G:TF603L0.998
9:82997125:A:GF603L0.998
9:82998383:T:AD596V0.998
9:82998387:A:GW595R0.998
9:82998387:A:TW595R0.998
9:83000249:C:TG548E0.998
9:83000250:C:AG548W0.998
9:82990438:A:CS690R0.997
9:82990438:A:TS690R0.997
9:82990440:T:GS690R0.997
9:82992910:G:TA679D0.997
9:82997029:A:GW635R0.997
9:82997029:A:TW635R0.997
9:82997076:A:GL619P0.997
9:82998382:A:CD596E0.997
9:82998382:A:TD596E0.997
9:82998383:T:CD596G0.997
9:82998384:C:GD596H0.997
9:82998389:A:GL594P0.997
9:83000231:T:AK554M0.997
9:83000232:T:GK554Q0.997
9:83000234:C:TG553E0.997
9:83000235:C:AG553W0.997
9:83009731:A:GL290P0.997
9:82990391:C:GR706P0.996
9:82990395:C:GA705P0.996
9:82992981:C:AK655N0.996

dbSNP variants (sampled 300 via entrez): RS1000014293 (9:83033872 C>T), RS1000023606 (9:83120146 A>G), RS1000023799 (9:83200340 G>A), RS1000026376 (9:83073745 A>G), RS1000039906 (9:83170028 C>G,T), RS1000045823 (9:83158496 T>C), RS1000054957 (9:83199941 C>T), RS1000058055 (9:82981055 T>C,G), RS1000061700 (9:83216872 T>C), RS1000074287 (9:83066775 TAGAA>T), RS1000075272 (9:83078239 T>C), RS1000095239 (9:83030623 T>C), RS1000124194 (9:83087982 A>G), RS1000144925 (9:83108681 C>A,T), RS1000158307 (9:82997363 A>C)

Disease associations

OMIM: gene MIM:611344 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

9 associations (top):

StudyTraitp-value
GCST001762_493Obesity-related traits8.000000e-06
GCST003773_8Loneliness (multivariate analysis)4.000000e-07
GCST005024_43Pursuit maintenance gain8.000000e-07
GCST006138_5Resting-state electroencephalogram vigilance3.000000e-06
GCST007576_102Chronotype3.000000e-10
GCST007692_83Chronic obstructive pulmonary disease2.000000e-08
GCST008526_11Coffee consumption6.000000e-07
GCST010321_16PR interval8.000000e-10
GCST012034_7Sleep (1/2-day periodicity)2.000000e-08

EFO canonical traits (7, from GWAS)

EFO IDTrait name
EFO:0005109energy expenditure
EFO:0007865loneliness measurement
EFO:0008433pursuit maintenance gain measurement
EFO:0004357electroencephalogram measurement
EFO:0008328chronotype measurement
EFO:0006781coffee consumption measurement
EFO:0004462PR interval

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

50 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression6
trichostatin Aaffects cotreatment, increases expression3
Cadmium Chlorideincreases expression, decreases expression3
methylmercuric chlorideincreases expression2
sodium arsenitedecreases expression2
entinostatincreases expression, affects cotreatment2
Panobinostatincreases expression, affects cotreatment2
Benzo(a)pyreneaffects methylation, decreases methylation2
Estradioldecreases expression, affects cotreatment2
Phenylmercuric Acetateaffects cotreatment, increases expression2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxideincreases expression, decreases expression2
terbufosincreases methylation1
benzo(e)pyreneaffects methylation1
2,3-bis(3’-hydroxybenzyl)butyrolactoneaffects cotreatment, decreases expression1
aflatoxin B2affects methylation1
mercuric bromideaffects cotreatment, increases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
belinostatincreases expression1
abrineincreases expression1
dorsomorphinincreases expression, affects cotreatment1
jinfukangaffects cotreatment, decreases expression1
Resveratroldecreases expression, affects cotreatment1
Temozolomidedecreases expression1
Air Pollutantsincreases abundance, increases expression1
Cisplatinaffects cotreatment, decreases expression1
Coumestrolaffects cotreatment, decreases expression1
Demecolcineincreases expression1
Fonofosincreases methylation1
Ethyl Methanesulfonateincreases expression1
Formaldehydeincreases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.