Gene Gene information from NCBI Gene database.
Entrez ID 4010
Gene name LIM homeobox transcription factor 1 beta
Gene symbol LMX1B
Synonyms (NCBI Gene)
FSGS10LMX1.2NPS1
Chromosome 9
Chromosome location 9q33.3
Summary This gene encodes a member of LIM-homeodomain family of proteins containing two N-terminal zinc-binding LIM domains, 1 homeodomain, and a C-terminal glutamine-rich domain. It functions as a transcription factor, and is essential for the normal development
SNPs SNP information provided by dbSNP.
23
SNP ID Visualize variation Clinical significance Consequence
rs121909486 C>A,T Pathogenic Coding sequence variant, synonymous variant, missense variant
rs121909487 C>T Pathogenic Coding sequence variant, stop gained
rs121909488 G>T Pathogenic Coding sequence variant, missense variant
rs121909490 C>T Pathogenic Coding sequence variant, stop gained
rs121909491 G>A Pathogenic Coding sequence variant, missense variant
miRNA miRNA information provided by mirtarbase database.
703
miRTarBase ID miRNA Experiments Reference
MIRT656719 hsa-miR-4512 HITS-CLIP 23824327
MIRT656717 hsa-miR-3918 HITS-CLIP 23824327
MIRT656718 hsa-miR-1224-3p HITS-CLIP 23824327
MIRT656716 hsa-miR-6734-3p HITS-CLIP 23824327
MIRT656715 hsa-miR-4297 HITS-CLIP 23824327
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
25
GO ID Ontology Definition Evidence Reference
GO:0000785 Component Chromatin ISA
GO:0000977 Function RNA polymerase II transcription regulatory region sequence-specific DNA binding IBA
GO:0000977 Function RNA polymerase II transcription regulatory region sequence-specific DNA binding ISS
GO:0000981 Function DNA-binding transcription factor activity, RNA polymerase II-specific IBA
GO:0000981 Function DNA-binding transcription factor activity, RNA polymerase II-specific IEA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
602575 6654 ENSG00000136944
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
O60663
Protein name LIM homeobox transcription factor 1-beta (LIM/homeobox protein 1.2) (LMX-1.2) (LIM/homeobox protein LMX1B)
Protein function Transcription factor involved in the regulation of podocyte-expressed genes (PubMed:24042019, PubMed:28059119). Essential for the specification of dorsal limb fate at both the zeugopodal and autopodal levels. {ECO:0000269|PubMed:24042019, ECO:00
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF00412 LIM 56 111 LIM domain Domain
PF00412 LIM 115 173 LIM domain Domain
PF00046 Homeodomain 220 276 Homeodomain Domain
Tissue specificity TISSUE SPECIFICITY: Expressed in most tissues. Highest levels in testis, thyroid, duodenum, skeletal muscle, and pancreatic islets.
Sequence
MDIATGPESLERCFPRGQTDCAKMLDGIKMEEHALRPGPATLGVLLGSDCPHPAVCEGCQ
RPISDRFLMRVNESSWHEECLQCAACQQALTTSCYFRDRKLYCKQDYQQLF
AAKCSGCME
KIAPTEFVMRALECVYHLGCFCCCVCERQLRKGDEFVLKEGQLLCKGDYEKEK
DLLSSVS
PDESDSVKSEDEDGDMKPAKGQGSQSKGSGDDGKDPRRPKRPRTILTTQQRRAFKASFEV
SSKPCRKVRETLAAETGLSVRVVQVWFQNQRAKMKK
LARRHQQQQEQQNSQRLGQEVLSS
RMEGMMASYTPLAPPQQQIVAMEQSPYGSSDPFQQGLTPPQMPGDHMNPYGNDSIFHDID
SDTSLTSLSDCFLGSSDVGSLQARVGNPIDRLYSMQSSYFAS
Sequence length 402
Interactions View interactions
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
44
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
Autosomal recessive Alport syndrome Likely pathogenic; Pathogenic rs121909490 RCV006449352
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Inherited focal segmental glomerulosclerosis Pathogenic rs1191455921 RCV003994037
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Lipoid nephrosis Likely pathogenic; Pathogenic rs1191455921 RCV002260131
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
LMX1B-related disorder Pathogenic; Likely pathogenic rs2490517671, rs121909491, rs2030200763, rs2490682185, rs2490687634, rs1835285052, rs1835287461, rs1835285480, rs2490689989, rs2490682241, rs1191455921 RCV003973630
RCV004748508
RCV003399638
RCV003416732
RCV003402815
View all (7 more)
★★★★★
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
BREAST CANCER GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
BREAST CARCINOMA GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
CHRONIC OBSTRUCTIVE PULMONARY DISEASE GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
CLUBFOOT CTD
★★☆☆☆
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
9q33.3q34.11 microdeletion syndrome 9q33.3q34.11 microdeletion syndrome Orphanet
★☆☆☆☆
Found in Text Mining only
Acquired cubitus valgus Cubitus valgus HPO_DG
★☆☆☆☆
Found in Text Mining only
ANONYCHIA Anonychia HPO_DG
★☆☆☆☆
Found in Text Mining only
Attention deficit hyperactivity disorder Attention Deficit Hyperactivity Disorder BEFREE 21184584
★☆☆☆☆
Found in Text Mining only
Autistic Disorder Autism BEFREE 21901133
★☆☆☆☆
Found in Text Mining only
Autistic Disorder Autism Pubtator 21901133 Associate
★☆☆☆☆
Found in Text Mining only
Behavior Disorders Behavior Disorders CTD_human_DG 20199424
★☆☆☆☆
Found in Text Mining only
Blepharoptosis Ptosis HPO_DG
★☆☆☆☆
Found in Text Mining only
Bone Diseases Bone disease Pubtator 26395556 Associate
★☆☆☆☆
Found in Text Mining only
Breast Carcinoma Breast Carcinoma GWASCAT_DG 29059683
★★☆☆☆
Found in Text Mining + Unknown/Other Associations