LMX1B

LIM homeobox transcription factor 1 beta, the group of LIM class homeoboxes

Basic information

Region (hg38): 9:126613928-126701032

Previous symbols: [ "NPS1" ]

Links

ENSG00000136944 ∙ NCBI:4010 ∙ OMIM:602575 ∙ HGNC:6654 ∙ Uniprot:O60663 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• nail-patella syndrome (Definitive), mode of inheritance: AD
• nail-patella syndrome (Strong), mode of inheritance: AD
• nail-patella syndrome (Supportive), mode of inheritance: AD
• nail-patella-like renal disease (Supportive), mode of inheritance: AD
• nail-patella syndrome (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Nail-patella syndrome; Focal segmental glomerulosclerosis 10	AD	Ophthalmologic; Pharmacogenomic; Renal	In Nail-patella syndrome, individuals may have open-angle glaucoma, and surveillance and appropriate treatment may be beneficial; Agents that may contribute to glaucoma (as well as NSAIDs as relates to renal function) should be avoided; Medical treatment (eg, ACE inhibitors) may be beneficial in terms of affecting the progression of renal disease; Renal transplantation has been described; In Focal segmental glomerulosclerosis, recognition of disease may allow early management, and renal transplant has been described	Dermatologic; Musculoskeletal; Ophthalmologic; Renal	9590287; 9618165; 15928687; 17515884; 18414507; 20301311; 21850167; 23687361; 32356190; 32791958
Onset may typically be during adulthood, though surveillance earlier may be warranted given reports of affected individuals in the 3rd decade

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the LMX1B gene.

• not_provided (424 variants)
• Nail-patella_syndrome (147 variants)
• Nail-patella-like_renal_disease (80 variants)
• Inborn_genetic_diseases (50 variants)
• LMX1B-related_disorder (33 variants)
• not_specified (17 variants)
• Focal_segmental_glomerulosclerosis (4 variants)
• Kidney_disorder (2 variants)
• Inherited_focal_segmental_glomerulosclerosis (1 variants)
• Neurodevelopmental_disorder (1 variants)
• Lipoid_nephrosis (1 variants)
• Nephrotic_syndrome (1 variants)
• Autosomal_recessive_Alport_syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the LMX1B gene is commonly pathogenic or not. These statistics are base on transcript: NM_001174147.2. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			5	94	3	102
missense	22	24	157	16		219
nonsense	37	3				40
start loss						0
frameshift	35	9				44
splice donor/acceptor (+/-2bp)	13	3	4	1		21
Total	107	39	166	111	3

Highest pathogenic variant AF is 0.000038558144

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
LMX1B	protein_coding	protein_coding	ENST00000355497	8	86590

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125704	0	3	125707	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.02	169	261	0.648	0.0000168	2624
Missense in Polyphen		43	99.872	0.43055		1013
Synonymous	-0.810	128	117	1.10	0.00000854	759
Loss of Function	3.56	4	22.1	0.181	0.00000120	214

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000882	0.0000882
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Essential for the specification of dorsal limb fate at both the zeugopodal and autopodal levels.
• Pathway: Primary Focal Segmental Glomerulosclerosis FSGS;Dopaminergic Neurogenesis;Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways (Consensus)

Recessive Scores

• pRec: 0.350

Intolerance Scores

• loftool: 0.0982
• rvis_EVS: -0.85
• rvis_percentile_EVS: 11.06

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.980

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Zebrafish Information Network

• Gene name: lmx1ba
• Affected structure: glutamatergic neuron
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: in utero embryonic development;regulation of transcription, DNA-templated;multicellular organism development;dorsal/ventral pattern formation;neuron differentiation;positive regulation of transcription by RNA polymerase II;dopaminergic neuron differentiation
• Cellular component: nucleus
• Molecular function: RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;protein binding;metal ion binding