Free for academic non-profit institutions. Other users need a Commercial license
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 of dorsal limb structures, the glomerular basement membrane, the anterior segment of the eye, and dopaminergic and serotonergic neurons. Mutations in this gene are associated with nail-patella syndrome. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2010]
LMX1B (LIM Homeobox Transcription Factor 1 Beta) is a Protein Coding gene. Diseases associated with LMX1B include Nail-Patella Syndrome and Focal Segmental Glomerulosclerosis 10. Among its related pathways are Primary Focal Segmental Glomerulosclerosis FSGS and Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways. Gene Ontology (GO) annotations related to this gene include DNA-binding transcription factor activity and sequence-specific DNA binding. An important paralog of this gene is LMX1A.
GO ID | Qualified GO term | Evidence | PubMed IDs |
---|---|---|---|
GO:0000977 | RNA polymerase II regulatory region sequence-specific DNA binding | ISS | -- |
GO:0000981 | DNA-binding transcription factor activity, RNA polymerase II-specific | ISS | -- |
GO:0003677 | DNA binding | IEA | -- |
GO:0003700 | DNA-binding transcription factor activity | IDA | 10767331 |
GO:0005515 | protein binding | IPI | 12792813 |
GO ID | Qualified GO term | Evidence | PubMed IDs |
---|---|---|---|
GO:0000785 | chromatin | ISA | -- |
GO:0005634 | nucleus | IBA,IDA | 10767331 |
SuperPathway | Contained pathways | ||
---|---|---|---|
1 | Dopaminergic Neurogenesis | ||
2 | Primary Focal Segmental Glomerulosclerosis FSGS | ||
3 | Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways |
GO ID | Qualified GO term | Evidence | PubMed IDs |
---|---|---|---|
GO:0001701 | in utero embryonic development | NAS | 12792813 |
GO:0006355 | regulation of transcription, DNA-templated | IDA | 10767331 |
GO:0006357 | regulation of transcription by RNA polymerase II | IBA | 21873635 |
GO:0007275 | multicellular organism development | NAS | 9590287 |
GO:0009953 | dorsal/ventral pattern formation | ISS | -- |
ExUns: | 1 | ^ | 2 | ^ | 3 | ^ | 4 | ^ | 5 | ^ | 6 | ^ | 7 | ^ | 8 | ^ | 9a | · | 9b | ^ | 10 |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
SP1: | - | - | - | ||||||||||||||||||
SP2: | - | - | |||||||||||||||||||
SP3: |
This gene was present in the common ancestor of animals.
Organism | Taxonomy | Gene | Similarity | Type | Details |
---|---|---|---|---|---|
Chimpanzee (Pan troglodytes) |
Mammalia | LMX1B 30 31 |
|
OneToOne | |
Oppossum (Monodelphis domestica) |
Mammalia | LMX1B 31 |
|
OneToOne | |
Dog (Canis familiaris) |
Mammalia | LMX1B 30 31 |
|
OneToOne | |
Platypus (Ornithorhynchus anatinus) |
Mammalia | LMX1B 31 |
|
OneToOne | |
Cow (Bos Taurus) |
Mammalia | LMX1B 30 31 |
|
OneToOne | |
Rat (Rattus norvegicus) |
Mammalia | Lmx1b 30 |
|
||
Mouse (Mus musculus) |
Mammalia | Lmx1b 30 17 31 |
|
OneToOne | |
Chicken (Gallus gallus) |
Aves | LMX1B 30 31 |
|
OneToOne | |
Lizard (Anolis carolinensis) |
Reptilia | LMX1B 31 |
|
OneToOne | |
Tropical Clawed Frog (Silurana tropicalis) |
Amphibia | LOC100495130 30 |
|
||
Str.18490 30 |
|
||||
Zebrafish (Danio rerio) |
Actinopterygii | lmx1ba 31 |
|
OneToMany | |
lmx1bb 30 31 |
|
OneToMany | |||
Fruit Fly (Drosophila melanogaster) |
Insecta | CG4328 31 32 |
|
ManyToMany | |
CG32105 31 |
|
ManyToMany | |||
Worm (Caenorhabditis elegans) |
Secernentea | lim-6 30 31 32 |
|
OneToMany | |
Sea Squirt (Ciona savignyi) |
Ascidiacea | -- 31 |
|
ManyToMany | |
-- 31 |
|
ManyToMany | |||
Sea Vase (Ciona intestinalis) |
Ascidiacea | Cin.235 30 |
|
SNP ID | Clinical significance and condition | Chr 09 pos | Variation | AA Info | Type |
---|---|---|---|---|---|
870908 | Pathogenic: not provided | 126,615,478(+) |
G/T NM_001174147.2(LMX1B):c.235G>T (p.Glu79Ter) |
NONSENSE | |
912632 | Uncertain Significance: Nail-patella syndrome | 126,693,733(+) |
G/A NM_001174147.2(LMX1B):c.820-13G>A |
INTRON | |
912633 | Likely Benign: Nail-patella syndrome | 126,695,885(+) |
G/T NM_001174147.2(LMX1B):c.933G>T (p.Pro311=) |
SYNONYMOUS | |
912673 | Uncertain Significance: Nail-patella syndrome | 126,696,737(+) |
C/T NM_001174147.2(LMX1B):c.*286C>T |
THREE_PRIME_UTR | |
912674 | Uncertain Significance: Nail-patella syndrome | 126,696,768(+) |
G/A NM_001174147.2(LMX1B):c.*317G>A |
THREE_PRIME_UTR |
Variant ID | Type | Subtype | PubMed ID |
---|---|---|---|
dgv1234n67 | CNV | gain | 20364138 |
dgv12868n54 | CNV | loss | 21841781 |
dgv12869n54 | CNV | loss | 21841781 |
esv2659178 | CNV | deletion | 23128226 |
esv2739046 | CNV | deletion | 23290073 |
esv3576705 | CNV | gain | 25503493 |
esv3621766 | CNV | gain | 21293372 |
esv3621769 | CNV | loss | 21293372 |
nsv1113016 | CNV | deletion | 24896259 |
nsv466568 | CNV | loss | 19166990 |
nsv517494 | CNV | loss | 19592680 |
nsv528719 | CNV | loss | 19592680 |
nsv615316 | CNV | loss | 21841781 |
nsv6718 | CNV | deletion | 18451855 |
nsv825080 | CNV | gain | 20364138 |
nsv825083 | CNV | gain | 20364138 |
nsv831723 | CNV | gain+loss | 17160897 |
nsv951764 | CNV | deletion | 24416366 |
Disorder | Aliases | PubMed IDs |
---|---|---|
nail-patella syndrome |
|
|
focal segmental glomerulosclerosis 10 |
|
|
dravet syndrome |
|
|
stxbp1 encephalopathy |
|
|
developmental and epileptic encephalopathy 4 |
|
|