LMX1B LIM homeobox transcription factor 1 beta [Homo sapiens (human)] - Gene

Summary

Official Symbol: LMX1Bprovided by HGNC
Official Full Name: LIM homeobox transcription factor 1 betaprovided by HGNC
Primary source: HGNC:HGNC:6654
See related: Ensembl:ENSG00000136944 MIM:602575; AllianceGenome:HGNC:6654
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: NPS1; FSGS10; LMX1.2
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 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]
Expression: Biased expression in salivary gland (RPKM 1.8), kidney (RPKM 0.4) and 3 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 9q33.3

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	9	NC_000009.12 (126613928..126701032)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	9	NC_060933.1 (138819355..138906454)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	9	NC_000009.11 (129376207..129463311)

Chromosome 9 - NC_000009.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

De novo enhancer deletion of LMX1B produces a mild nail-patella clinical phenotype.
Title: De novo enhancer deletion of LMX1B produces a mild nail-patella clinical phenotype.
ATG8-dependent LMX1B-autophagy crosstalk shapes human midbrain dopaminergic neuronal resilience.
Title: ATG8-dependent LMX1B-autophagy crosstalk shapes human midbrain dopaminergic neuronal resilience.
Knockdown of LMX1B Suppressed Cell Apoptosis and Inflammatory Response in IL-1beta-Induced Human Osteoarthritis Chondrocytes through NF-kappaB and NLRP3 Signal Pathway.
Title: Knockdown of LMX1B Suppressed Cell Apoptosis and Inflammatory Response in IL-1β-Induced Human Osteoarthritis Chondrocytes through NF-κB and NLRP3 Signal Pathway.
Association analysis of variants rs35934224 in TXNRD2 and rs6478746 in LMX1B in primary angle-closure and pseudoexfoliation glaucoma.
Title: Association analysis of variants rs35934224 in TXNRD2 and rs6478746 in LMX1B in primary angle-closure and pseudoexfoliation glaucoma.
LMX1B Activated Circular RNA GFRA1 Modulates the Tumorigenic Properties and Immune Escape of Prostate Cancer.
Title: LMX1B Activated Circular RNA GFRA1 Modulates the Tumorigenic Properties and Immune Escape of Prostate Cancer.
hsa-miR-206b Involves in the Development of Papillary Thyroid Carcinoma via Targeting LMX1B.
Title: hsa-miR-206b Involves in the Development of Papillary Thyroid Carcinoma via Targeting LMX1B.
Long noncoding RNA SNHG3 promotes glioma tumorigenesis by sponging miR-485-5p to upregulate LMX1B expression.
Title: Long noncoding RNA SNHG3 promotes glioma tumorigenesis by sponging miR-485-5p to upregulate LMX1B expression.
LMX1B Locus Associated with Low-Risk Baseline Glaucomatous Features in the POAAGG Study.
Title: LMX1B Locus Associated with Low-Risk Baseline Glaucomatous Features in the POAAGG Study.
Whole-Exome Sequencing Solved over 2-Decade Kidney Disease Enigma.
Title: Whole-Exome Sequencing Solved over 2-Decade Kidney Disease Enigma.
Identification of limb-specific Lmx1b auto-regulatory modules with Nail-patella syndrome pathogenicity.
Title: Identification of limb-specific Lmx1b auto-regulatory modules with Nail-patella syndrome pathogenicity.

Submit: New GeneRIF Correction See all GeneRIFs (54)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Nail-patella syndrome MedGen: C0027341 OMIM: 161200 GeneReviews: Nail-Patella Syndrome	Compare labs
Nail-patella-like renal disease MedGen: C0403548 OMIM: 256020 GeneReviews: Not available	Compare labs

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2020-11-10) ClinGen Genome Curation Page Haploinsufficency Sufficient evidence for dosage pathogenicity (Last evaluated 2020-11-10) ClinGen Genome Curation PagePubMed

EBI GWAS Catalog

Description
Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index. EBI GWAS Catalog EBI GWAS CatalogPubMed
Variability in the common genetic architecture of social-communication spectrum phenotypes during childhood and adolescence. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

NoName (e-PCR)
- UniSTS:480873

RH80030 (e-PCR)
- UniSTS:87680

NoName (e-PCR)
- UniSTS:483257

D9S112 (e-PCR)
- UniSTS:147156

SHGC-147195 (e-PCR)
- UniSTS:172767

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA-binding transcription factor activity	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISA Inferred from Sequence Alignment more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISS Inferred from Sequence or Structural Similarity more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in dopaminergic neuron differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in dorsal/ventral pattern formation	ISS Inferred from Sequence or Structural Similarity more info
involved_in neuron differentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in neuron differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of transcription by RNA polymerase II	TAS Traceable Author Statement more info	PubMed
involved_in regulation of DNA-templated transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
part_of chromatin	ISA Inferred from Sequence Alignment more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: LIM homeobox transcription factor 1-beta

Names: LIM/homeobox protein 1.2; LMX-1.2

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_017039.1 RefSeqGene

Range

4486..91590

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_1014

mRNA and Protein(s)

NM_001174146.2 → NP_001167617.1 LIM homeobox transcription factor 1-beta isoform 3

Status: REVIEWED

Description

Transcript Variant: This variant (3) uses an alternate donor splice site at an internal coding exon compared to variant 1, resulting in a longer isoform (3) containing an additional 11 aa protein segment compared to isoform 1.

Source sequence(s)

AL161731, AL161908, BC143801, EL952935

Consensus CDS

CCDS55343.1

UniProtKB/TrEMBL

B7ZLH2

Related

ENSP00000347684.5, ENST00000355497.10

Conserved Domains (3) summary

cd09371
Location:56 → 108

LIM1_Lmx1b; The first LIM domain of Lmx1b

cd09378
Location:115 → 169

LIM2_Lmx1a_Lmx1b; The second LIM domain of Lmx1a and Lmx1b

pfam00046
Location:222 → 275

Homeobox; Homeobox domain
NM_001174147.2 → NP_001167618.1 LIM homeobox transcription factor 1-beta isoform 2

See identical proteins and their annotated locations for NP_001167618.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate donor splice site at the penultimate coding exon compared to variant 1, resulting in a longer isoform (2) containing an additional 7 aa protein segment compared to isoform 1.

Source sequence(s)

AL161731, AL161908, BC069588, BC113491, EL952935

Consensus CDS

CCDS55342.1

UniProtKB/Swiss-Prot

F8W7W6, O60663, O75463, Q5JU95, Q6ISC9

UniProtKB/TrEMBL

Q6ISE0

Related

ENSP00000362573.3, ENST00000373474.9

Conserved Domains (3) summary

cd09371
Location:56 → 108

LIM1_Lmx1b; The first LIM domain of Lmx1b

cd09378
Location:115 → 169

LIM2_Lmx1a_Lmx1b; The second LIM domain of Lmx1a and Lmx1b

pfam00046
Location:222 → 276

Homeobox; Homeobox domain
NM_002316.4 → NP_002307.2 LIM homeobox transcription factor 1-beta isoform 1

See identical proteins and their annotated locations for NP_002307.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes isoform 1.

Source sequence(s)

AL161731, AL161908, BC113491, EL952935

Consensus CDS

CCDS6866.2

UniProtKB/TrEMBL

Q6ISE0

Related

ENSP00000436930.1, ENST00000526117.6

Conserved Domains (3) summary

cd09371
Location:56 → 108

LIM1_Lmx1b; The first LIM domain of Lmx1b

cd09378
Location:115 → 169

LIM2_Lmx1a_Lmx1b; The second LIM domain of Lmx1a and Lmx1b

pfam00046
Location:222 → 276

Homeobox; Homeobox domain