• 3
    Haplo
    Score
  • 0
    Triplo
    Score

Gene Facts External Data Attribution

HGNC Symbol
LMX1B (HGNC:6654) HGNC Entrez Ensembl OMIM UCSC Uniprot GeneReviews LOVD LSDB ClinVar
HGNC Name
LIM homeobox transcription factor 1 beta
Gene type
protein-coding gene
Locus type
gene with protein product
Previous symbols
NPS1
Alias symbols
No aliases found
%HI
2.11(Read more about the DECIPHER Haploinsufficiency Index)
pLI
0.75(Read more about gnomAD pLI score)
LOEUF
0.42(Read more about gnomAD LOEUF score)
Cytoband
9q33.3
Genomic Coordinates
GRCh37/hg19: chr9:129376207-129463311 NCBI Ensembl UCSC
GRCh38/hg38: chr9:126613928-126701032 NCBI Ensembl UCSC
MANE Select Transcript
NM_001174147.2 ENST00000373474.9 (Read more about MANE Select)
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:0000269|PubMed:28059119}. (Source: Uniprot)

Dosage Sensitivity Summary (Gene)

Dosage ID:
ISCA-36879
Curation Status:
Complete
Issue Type:
Dosage Curation - Gene
Haploinsufficiency:
Sufficient Evidence for Haploinsufficiency (3)
Triplosensitivity:
No Evidence for Triplosensitivity (0)
Last Evaluated:
11/10/2020

Haploinsufficiency (HI) Score Details

HI Score:
3
HI Evidence Strength:
Sufficient Evidence for Haploinsufficiency (Disclaimer)
HI Disease:
HI Evidence:
  • PUBMED: 9618165
    Vollrath et al. (1998) describe variants identified in four families with nail-patella syndrome (NPS) and open-angle glaucoma, including 2 nonsense variants and 1 frameshift variant (2 bp deletion).
  • PUBMED: 9837817
    McIntosh et al. (1998) screened a cohort of 41 NPS families for LMX1B variants. A total of 25 variants were identified in 37 families, including 5 frameshift variants, 6 previously unreported nonsense variants, and 5 canonical splice site variants.
  • PUBMED: 18414507
    Bongers et al. (2008) searched for deletions of the entire LMX1B gene in families with the classical NPS phenotype by MLPA, and found deletions in three patients: 1) a de novo deletion limited to the LMX1B gene in patient 1; 2) an inherited deletion including some flanking regions in patient 2; and 3) a deletion of exons 3–8 in patient 3.
HI Evidence Comments:
Additional evidence includes: PMID: 31053111 Yan et al. (2019) identified a small, novel, heterozygous deletion within exon 4 of LMX1B, c.712_714delTTC, in a five-generation NPS pedigree. The variant resulted in a deletion of the conserved amino acid phenylalanine at codon 238 (p.Phe238del), which is located in the homeodomain of LMX1B. The authors postulate that this may abolish DNA binding with the molecule. PMID: 20531206 Marini et al, (2019) performed LMX1B screening on 20 Nail-Patella syndrome patients. LMX1B variants were found in 17 patients, including 1 frameshift and 2 nonsense variants. PMID: 15498463 Dunston et al. (2004) sequenced LMX1B exons and immediate flanking intron sequence in 105 unrelated individuals with NPS and identified 47 novel variants (table 1), including 13 frameshift and 6 nonsense variants.

Triplosensitivity (TS) Score Details

TS Score:
0
TS Evidence Strength:
No Evidence for Triplosensitivity (Disclaimer)

Genomic View

Select assembly: (NC_000009.11) (NC_000009.12)