Nail-patella-like renal disease

Summary

Nail-patella-like renal disease (MONDO:0009724) is a disease with 1 cohort gene.

At a glance

• Prevalence: <1 / 1 000 000 (Worldwide) [Orphanet-validated]
• Cohort genes: 1
• ClinVar variants: 83
• Phenotypes (HPO): 6

Clinical features

Epidemiology

Prevalence records

2 prevalence record(s), Orphanet:

Type	Class	Value	Geography	Validation
Cases/families		3	Worldwide	Validated
Point prevalence	<1 / 1 000 000		Worldwide	Validated

Signs & symptoms

Clinical features (HPO)

6 HPO clinical features (Orphanet curated; top 6 by frequency):

HPO ID	Term	Frequency
HP:0000083	Renal insufficiency	Very frequent (80-99%)
HP:0000093	Proteinuria	Very frequent (80-99%)
HP:0000822	Hypertension	Very frequent (80-99%)
HP:0002907	Microscopic hematuria	Very frequent (80-99%)
HP:0004322	Short stature	Very frequent (80-99%)
HP:0100820	Glomerulopathy	Very frequent (80-99%)

Identifiers

Disease identifiers

Field	Value
Canonical name	nail-patella-like renal disease
Mondo ID	MONDO:0009724
MeSH	C537228
OMIM	256020
Orphanet	2613
SNOMED CT	236527004
UMLS	C0403548
MedGen	140789
GARD	0000321
Is cancer (heuristic)	no

Also known as: focal segmental glomerulosclerosis 10 · nail patella like renal disease · nail-patella-like renal disease · Salcedo syndrome

Data availability: 83 ClinVar variants · 1 GenCC gene-disease record.

Disease family

Classification path: disease › human disease › disease by etiologic mechanism › disease of genetic or genomic mechanism › hereditary disease › inherited kidney disorder › nail-patella-like renal disease

Related subtypes (25): familial juvenile hyperuricemic nephropathy, familial nephrotic syndrome, hereditary renal cell carcinoma, hereditary kidney oncocytoma, hereditary nephritis, inherited focal segmental glomerulosclerosis, prune belly syndrome, neurohypophyseal diabetes insipidus, fibronectin glomerulopathy, Liddle syndrome, familial renal glucosuria, renal tubular dysgenesis of genetic origin, proteinuria, low molecular weight, with hypercalciuria and nephrocalcinosis, nephrolithiasis, X-linked recessive, with renal failure, hypophosphatemic nephrolithiasis/osteoporosis 1, hypophosphatemic nephrolithiasis/osteoporosis 2, inherited renal tubular disease, renal agenesis, congenital anomaly of kidney and urinary tract, familial cystic renal disease, Alsing syndrome, inherited pseudohypoaldosteronism, Gitelman-like kidney tubulopathy due to mitochondrial DNA mutation, nephrolithiasis, calcium oxalate, inherited distal renal tubular acidosis

Genetics & variants

GWAS landscape

No GWAS associations recorded — common-variant (GWAS) studies don’t cover this disease (typical for Mendelian / rare diseases). See the curated gene cohort and Mendelian overlap below.

Variant details and genetic-evidence tiers

ClinVar germline variants

83 retrieved; paginated sample, class counts are floors:

40 uncertain significance, 12 conflicting classifications of pathogenicity, 9 benign/likely benign, 7 likely benign, 6 pathogenic, 3 benign, 3 likely pathogenic, 3 pathogenic/likely pathogenic

ClinVar	Variant (HGVS)	Gene	Classification	Review
3596446	NM_001174147.2(LMX1B):c.746G>A (p.Arg249Gln)	LMX1B	Pathogenic	criteria provided, multiple submitters, no conflicts
3720898	NM_001174147.2(LMX1B):c.229C>T (p.His77Tyr)	LMX1B	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
498798	NM_001174147.2(LMX1B):c.737G>A (p.Arg246Gln)	LMX1B	Pathogenic	criteria provided, multiple submitters, no conflicts
7000	NM_001174147.2(LMX1B):c.807C>A (p.Asn269Lys)	LMX1B	Pathogenic/Likely pathogenic	criteria provided, multiple submitters, no conflicts
7005	NM_001174147.2(LMX1B):c.244C>T (p.Gln82Ter)	LMX1B	Pathogenic	criteria provided, multiple submitters, no conflicts
7007	NM_001174147.2(LMX1B):c.668G>A (p.Arg223Gln)	LMX1B	Pathogenic	criteria provided, multiple submitters, no conflicts
812901	NM_001174147.2(LMX1B):c.737G>C (p.Arg246Pro)	LMX1B	Pathogenic/Likely pathogenic	no assertion criteria provided
976712	NM_001174147.2(LMX1B):c.706G>C (p.Ala236Pro)	LMX1B	Pathogenic	criteria provided, multiple submitters, no conflicts
988549	NM_001174147.2(LMX1B):c.325C>T (p.Gln109Ter)	LMX1B	Pathogenic	criteria provided, multiple submitters, no conflicts
3068346	NM_001174147.2(LMX1B):c.957del (p.Ile319fs)	LMX1B	Likely pathogenic	criteria provided, single submitter
4688017	NM_001174147.2(LMX1B):c.432C>A (p.Cys144Ter)	LMX1B	Likely pathogenic	criteria provided, single submitter
666319	NM_001174147.2(LMX1B):c.745C>G (p.Arg249Gly)	LMX1B	Likely pathogenic	criteria provided, multiple submitters, no conflicts
1006393	NM_001174147.2(LMX1B):c.874C>T (p.Arg292Trp)	LMX1B	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
1023525	NM_001174147.2(LMX1B):c.451C>T (p.Arg151Cys)	LMX1B	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
1035953	NM_001174147.2(LMX1B):c.958G>A (p.Val320Met)	LMX1B	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
1357819	NM_001174147.2(LMX1B):c.1201G>A (p.Ala401Thr)	LMX1B	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
1394734	NM_001174147.2(LMX1B):c.915G>A (p.Met305Ile)	LMX1B	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
1520811	NM_001174147.2(LMX1B):c.1153G>A (p.Val385Met)	LMX1B	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
2433493	NM_001174147.2(LMX1B):c.783C>T (p.Arg261=)	LMX1B	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
3596449	NM_001174147.2(LMX1B):c.929C>T (p.Thr310Met)	LMX1B	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
364887	NM_001174147.2(LMX1B):c.972G>C (p.Gln324His)	LMX1B	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
912633	NM_001174147.2(LMX1B):c.933G>T (p.Pro311=)	LMX1B	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
914598	NM_001174147.2(LMX1B):c.535G>A (p.Val179Met)	LMX1B	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
995576	NM_001174147.2(LMX1B):c.353G>A (p.Cys118Tyr)	LMX1B	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
1011992	NM_001174147.2(LMX1B):c.463G>A (p.Glu155Lys)	LMX1B	Uncertain significance	criteria provided, multiple submitters, no conflicts
1027208	NM_001174147.2(LMX1B):c.130G>A (p.Val44Met)	LMX1B	Uncertain significance	criteria provided, multiple submitters, no conflicts
1060826	NM_001174147.2(LMX1B):c.1052G>A (p.Gly351Glu)	LMX1B	Uncertain significance	criteria provided, multiple submitters, no conflicts
1316843	NM_001174147.2(LMX1B):c.508G>A (p.Glu170Lys)	LMX1B	Uncertain significance	criteria provided, multiple submitters, no conflicts
1361298	NM_001174147.2(LMX1B):c.1002G>T (p.Gln334His)	LMX1B	Uncertain significance	criteria provided, multiple submitters, no conflicts
1375664	NM_001174147.2(LMX1B):c.1084G>A (p.Asp362Asn)	LMX1B	Uncertain significance	criteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 6 · Orphanet: 3 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0

GenCC gene–disease validity (cohort genes)

the Disease column is the GenCC-asserted condition — a cohort gene’s strongest validity may be for a related predisposition syndrome.

Gene	Classification	Inheritance	Disease	Records
LMX1B	Definitive	Autosomal dominant	nail-patella syndrome	6

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
LMX1B	Orphanet:2613	Nail-patella-like renal disease
LMX1B	Orphanet:2614	Nail-patella syndrome
LMX1B	Orphanet:495818	9q33.3q34.11 microdeletion syndrome

Cohort genes → proteins

1 cohort genes, 1 distinct canonical proteins.

Evidence partition

Subset	Genes
multi_evidence	1

Cohort genes (full)

Symbol	HGNC	Ensembl	UniProt	Name	Evidence
LMX1B	HGNC:6654	ENSG00000136944	O60663	LIM homeobox transcription factor 1-beta	gencc,clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
LMX1B	LIM homeobox transcription factor 1-beta	Transcription factor involved in the regulation of podocyte-expressed genes.

Protein-family classification

Druggable: 0 · Difficult: 1 · Unknown: 0 · Druggable fraction: 0.0

Family distribution

Cohort families vs a genome-wide background (hypergeometric, BH-FDR; fold = observed/expected). Counts kept; sorted by enrichment, so the catch-all Other/Unknown bucket no longer leads.

Family	Genes	Fold	FDR
Transcription factor	1	8.3×	0.121

Per-gene assignment

Symbol	Family	Druggable?	EC	InterPro (top 3)
LMX1B	Transcription factor	no		HD, Znf_LIM, Homeodomain-like_sf

Expression context

Cohort genes with no expression data: 0.

1 cohort gene are a single-cell marker in ≥1 SCXA experiment.

Breadth distribution (Bgee present_calls)

Bucket	Genes
narrow (1-5 tissues)	0
moderate (6-20)	0
broad (>20)	1
unknown	0

Top tissues across cohort

Tissue	Cohort genes
male germ line stem cell (sensu Vertebrata) in testis	1
primordial germ cell in gonad	1
sural nerve	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
LMX1B	74	broad	marker	sural nerve, male germ line stem cell (sensu Vertebrata) in testis, primordial germ cell in gonad

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
LMX1B	1,514

Structural data

PDB: 0 · AlphaFold-only: 1 · No structure: 0

AlphaFold-only cohort genes (top 30 by pLDDT)

Symbol	UniProt	pLDDT
LMX1B	O60663	70.79

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 0. Enrichment computed across 1 evidence-associated genes (0 with Reactome annotation).

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 1 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO term	Cohort genes	Fold	FDR	Sample cohort genes
dopaminergic neuron differentiation	1	624.1×	0.007	LMX1B
dorsal/ventral pattern formation	1	421.3×	0.007	LMX1B
neuron differentiation	1	100.3×	0.020	LMX1B
regulation of DNA-templated transcription	1	31.6×	0.048	LMX1B
positive regulation of transcription by RNA polymerase II	1	14.9×	0.081	LMX1B
regulation of transcription by RNA polymerase II	1	11.7×	0.086	LMX1B

Therapeutics

Drug target analysis

Approved (phase 4): 0 · Phase ≥3: 0 · Phased (≥1): 0 · Undrugged: 1

Druggability breadth: 0 of 1 evidence-associated genes (0%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

Symbol	Molecules	Max phase
LMX1B	0	0

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 0.

Pharmacogenomics

Cohort genes with a PharmGKB record: 1; with CPIC/DPWG dosing guidelines: 0.

No cohort gene has a CPIC/DPWG genotype-guided dosing guideline (PharmGKB).

Chemical tractability of cohort targets

0 approved/phased compounds have measured bioactivity against a cohort gene (and aren’t yet in disease-level trials). This is a research / tractability signal, NOT a therapeutic recommendation — a bioactivity row often reflects off-target or screening binding (e.g. promiscuous kinase inhibitors against a cohort kinase), implying no disease mechanism.

Druggability pyramid

Cohort genes binned by druggability tier (high → low):

Tier	Definition	Genes	Symbols
A	Approved (phase 4 drug)	0
B	Phased (≥1) drug, not yet approved	0
C	Druggable family + PDB, no drug	0
D	Druggable family + AlphaFold only, no drug	0
E	Difficult family or no structure, no drug	1	LMX1B

Undrugged target profiles

1 cohort genes are undrugged. Ranked by ‘starting-point quality’ (assay depth + drugged-partner adjacency).

Symbol	ChEMBL assays	Drugged partners (top 3)
LMX1B	0	—

Clinical trials & evidence

Clinical trials

Clinical trials: 0.