Gene Gene information from NCBI Gene database.
Entrez ID 51132
Gene name Ring finger protein, LIM domain interacting
Gene symbol RLIM
Synonyms (NCBI Gene)
MRX61NY-REN-43RNF12TOKAS
Chromosome X
Chromosome location Xq13.2
Summary 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-repr
SNPs SNP information provided by dbSNP.
9
SNP ID Visualize variation Clinical significance Consequence
rs786205133 T>C Likely-pathogenic, pathogenic Missense variant, coding sequence variant
rs1569309449 G>A Pathogenic Coding sequence variant, missense variant
rs1569309459 G>A Pathogenic Coding sequence variant, missense variant
rs1569309460 C>T Pathogenic Coding sequence variant, missense variant
rs1569309474 G>C Pathogenic Coding sequence variant, missense variant
miRNA miRNA information provided by mirtarbase database.
1640
miRTarBase ID miRNA Experiments Reference
MIRT048396 hsa-miR-100-5p CLASH 23622248
MIRT047752 hsa-miR-10a-5p CLASH 23622248
MIRT046403 hsa-miR-15b-5p CLASH 23622248
MIRT044990 hsa-miR-186-5p CLASH 23622248
MIRT714107 hsa-miR-7849-3p HITS-CLIP 19536157
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
29
GO ID Ontology Definition Evidence Reference
GO:0000122 Process Negative regulation of transcription by RNA polymerase II IEA
GO:0003714 Function Transcription corepressor activity NAS 11013082
GO:0004842 Function Ubiquitin-protein transferase activity IDA 29742418, 33953269
GO:0004842 Function Ubiquitin-protein transferase activity IEA
GO:0004842 Function Ubiquitin-protein transferase activity ISS
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
300379 13429 ENSG00000131263
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q9NVW2
Protein name E3 ubiquitin-protein ligase RLIM (EC 2.3.2.27) (LIM domain-interacting RING finger protein) (RING finger LIM domain-binding protein) (R-LIM) (RING finger protein 12) (RING-type E3 ubiquitin transferase RLIM) (Renal carcinoma antigen NY-REN-43)
Protein function E3 ubiquitin-protein ligase. Acts as a negative coregulator for LIM homeodomain transcription factors by mediating the ubiquitination and subsequent degradation of LIM cofactors LDB1 and LDB2 and by mediating the recruitment the SIN3a/histone de
PDB 6W7Z , 6W9A , 6W9D
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF13639 zf-RING_2 568 611 Ring finger domain Domain
Tissue specificity TISSUE SPECIFICITY: Expressed in many tissues.
Sequence
MENSDSNDKGSGDQSAAQRRSQMDRLDREEAFYQFVNNLSEEDYRLMRDNNLLGTPGEST
EEELLRRLQQIKEGPPPQNSDENRGGDSSDDVSNGDSIIDWLNSVRQTGNTTRSGQRGNQ
SWRAVSRTNPNSGDFRFSLEINVNRNNGSQNSENENEPSARRSSGENVENNSQRQVENPR
SESTSARPSRSERNSTEALTEVPPTRGQRRARSRSPDHRRTRARAERSRSPLHPMSEIPR
RSHHSISSQTFEHPLVNETEGSSRTRHHVTLRQQISGPELLSRGLFAASGTRNASQGAGS
SDTAASGESTGSGQRPPTIVLDLQVRRVRPGEYRQRDSIASRTRSRSQTPNNTVTYESER
GGFRRTFSRSERAGVRTYVSTIRIPIRRILNTGLSETTSVAIQTMLRQIMTGFGELSYFM
YSDSDSEPTGSVSNRNMERAESRSGRGGSGGGSSSGSSSSSSSSSSSSSSSSSSSSPSSS
SGGESSETSSDLFEGSNEGSSSSGSSGARREGRHRAPVTFDESGSLPFLSLAQFFLLNED
DDDQPRGLTKEQIDNLAMRSFGENDALKTCSVCITEYTEGNKLRKLPCSHEYHVHCIDRW
LSENSTCPICR
RAVLASGNRESVV
Sequence length 624
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
  Reactome
    Antigen processing: Ubiquitination & Proteasome degradation
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
20
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Global developmental delay Pathogenic rs786205133 RCV001526527
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Intellectual disability, X-linked 61 Likely pathogenic; Pathogenic rs2147372360, rs786205133, rs1569309474, rs1569309776, rs1569309459, rs1569309460, rs1569309816, rs1569309449, rs1569309484, rs2079618652 RCV001542628
RCV000207499
RCV000239584
RCV000239497
RCV000239547
View all (5 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Non-syndromic X-linked intellectual disability Pathogenic; Likely pathogenic rs786205133, rs1569309776 RCV000170337
RCV004017569
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
Cervical cancer Likely benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Familial cancer of breast Likely benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Joubert syndrome Benign; Likely benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Lung cancer Likely benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Anxiety Anxiety Disorder HPO_DG
★☆☆☆☆
Found in Text Mining only
Autistic Disorder Autism CLINVAR_DG 25735484
★☆☆☆☆
Found in Text Mining only
Behavior Disorders Behavior Disorders BEFREE 29728705
★☆☆☆☆
Found in Text Mining only
Brachydactyly Brachydactyly HPO_DG
★☆☆☆☆
Found in Text Mining only
Breast Neoplasms Breast neoplasm Pubtator 19117995 Associate
★☆☆☆☆
Found in Text Mining only
Carcinoma Hepatocellular Hepatocellular carcinoma Pubtator 37132043 Stimulate
★☆☆☆☆
Found in Text Mining only
Carcinoma of lung Lung carcinoma BEFREE 30072581
★☆☆☆☆
Found in Text Mining only
Cryptorchidism Cryptorchidism HPO_DG
★☆☆☆☆
Found in Text Mining only
Deglutition Disorders Dysphagia HPO_DG
★☆☆☆☆
Found in Text Mining only
Dwarfism Dwarfism HPO_DG
★☆☆☆☆
Found in Text Mining only