LMX1B |
- 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
- 1(Read more about gnomAD pLI score)
- LOEUF
- 0.41(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
ClinGen Curation ID:
CCID:007412
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:
- Nail-patella syndrome Monarch
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)