Seroatlas · Human Serome Atlas

RLIM

E3 ubiquitin-protein ligase RLIM

Also known as: MGC15161, NY-REN-43, RNF12, RNF12_HUMAN

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession: Q9NVW2
Gene: RLIM
Ensembl: ENSG00000131263
Chromosome: X
Canonical length: 624 aa
Protein class: Disease related genes, Enzymes, Human disease related genes, Potential drug targets, Predicted intracellular proteins
Subcellular location: Nucleoplasm,Cytosol
Quaternary structure: Homodimer

OverviewNCBI Gene

The protein encoded by this gene is a RING-H2 zinc finger protein. It has been shown to be an E3 ubiquitin protein ligase that targets LIM domain binding 1 (LDB1/CLIM), and causes proteasome-dependent degradation of LDB1. This protein and LDB1 are co-repressors of LHX1/LIM-1, a homeodomain transcription factor. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Feb 2009]

Canonical amino-acid sequenceUniProt

624 residues, UniProt reviewed canonical sequence.

>Q9NVW2|RLIM
     1  MENSDSNDKG SGDQSAAQRR SQMDRLDREE AFYQFVNNLS EEDYRLMRDN NLLGTPGEST
    61  EEELLRRLQQ IKEGPPPQNS DENRGGDSSD DVSNGDSIID WLNSVRQTGN TTRSGQRGNQ
   121  SWRAVSRTNP NSGDFRFSLE INVNRNNGSQ NSENENEPSA RRSSGENVEN NSQRQVENPR
   181  SESTSARPSR SERNSTEALT EVPPTRGQRR ARSRSPDHRR TRARAERSRS PLHPMSEIPR
   241  RSHHSISSQT FEHPLVNETE GSSRTRHHVT LRQQISGPEL LSRGLFAASG TRNASQGAGS
   301  SDTAASGEST GSGQRPPTIV LDLQVRRVRP GEYRQRDSIA SRTRSRSQTP NNTVTYESER
   361  GGFRRTFSRS ERAGVRTYVS TIRIPIRRIL NTGLSETTSV AIQTMLRQIM TGFGELSYFM
   421  YSDSDSEPTG SVSNRNMERA ESRSGRGGSG GGSSSGSSSS SSSSSSSSSS SSSSSSPSSS
   481  SGGESSETSS DLFEGSNEGS SSSGSSGARR EGRHRAPVTF DESGSLPFLS LAQFFLLNED
   541  DDDQPRGLTK EQIDNLAMRS FGENDALKTC SVCITEYTEG NKLRKLPCSH EYHVHCIDRW
   601  LSENSTCPIC RRAVLASGNR ESVV

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against RLIM can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability: Intracellular
Secreted: No
Transmembrane segments: 0
Mean surface accessibility (rSASA): 0.57
Highest tissue expression: 39 nTPM

Expression across tissuesHPA

Tissue

bone marrow: 39 nTPM
cerebral cortex: 15 nTPM
adrenal gland: 11 nTPM
parathyroid gland: 11 nTPM
thyroid gland: 11 nTPM
thymus: 10 nTPM

Single-cell type

neutrophils: 191 nCPM
adrenal medulla cells: 96 nCPM
hematopoietic stem cells: 82 nCPM
megakaryocyte-erythroid progenitors: 81 nCPM
mast cells: 81 nCPM
neutrophil progenitors: 79 nCPM

Immune cell

basophil: 23 nTPM
neutrophil: 12 nTPM
intermediate monocyte: 7.5 nTPM
classical monocyte: 6 nTPM
eosinophil: 5.9 nTPM
non-classical monocyte: 5.7 nTPM

Brain region

hypothalamus: 54 nTPM
basal ganglia: 45 nTPM
cerebral cortex: 44 nTPM
pons: 44 nTPM
midbrain: 44 nTPM
choroid plexus: 43 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about RLIM.

Disease | AllUniProt

Conditions RLIM is implicated in, by any mechanism.

Tonne-Kalscheuer syndrome (TOKAS) MIM:300978

Disease | GeneticClinVar

12 pathogenic / likely-pathogenic of 184 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Intellectual disability, X-linked 61
Non-syndromic X-linked intellectual disability
Global developmental delay
Inborn genetic diseases
See cases

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance): 0.25
gnomAD pLI: 0.99
gnomAD missense Z: 2.42
DepMap mean gene effect: -0.1
DepMap dependency class: selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 5% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of RLIM in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads RLIM as an antibody target. Whether an autoantibody or antibody against RLIM could matter depends on whether native RLIM is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

RLIM is annotated as predominantly intracellular. Intracellular proteins are common autoantibody markers, becoming visible to the immune system after cell injury or altered processing, but are usually markers of disease rather than direct drivers.

Annotation status

The present source text does not explicitly label RLIM as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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