Renal tubular dysgenesis of genetic origin

disease
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Also known as genetic renal tubular dysgenesisrenal tubular dysgenesisRTD

Summary

Renal tubular dysgenesis of genetic origin (MONDO:0009970) is a disease caused by variants in ACE, AGT, AGTR1, and 1 other genes, with 6 cohort genes. The dominant Reactome pathway is Metabolism of Angiotensinogen to Angiotensins (3 cohort genes).

At a glance

  • Causal genes: ACE (GenCC Strong), AGT (GenCC Strong), AGTR1 (GenCC Strong), REN (GenCC Strong)
  • Cohort genes: 6
  • ClinVar variants: 544

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

FieldValue
Canonical namerenal tubular dysgenesis of genetic origin
Mondo IDMONDO:0009970
OMIM267430
Orphanet97369
ICD-11616055520
UMLSC5681536
MedGen1826125
GARD0016854
Is cancer (heuristic)no

Also known as: genetic renal tubular dysgenesis · renal tubular dysgenesis · renal tubular dysgenesis of genetic origin · RTD

Data availability: 544 ClinVar variants · 16 GenCC gene-disease records.

Disease family

An umbrella term covering 1 Mondo subtype.

Classification path: disease › human disease › disease by body system or component › urinary system disorderkidney disorderrenal tubular dysgenesisrenal tubular dysgenesis of genetic origin

Related subtypes (2): renal tubular dysgenesis due to twin-twin transfusion, drug-related renal tubular dysgenesis

Subtypes (1): renal tubular dysgenesis - ACE

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

544 retrieved; paginated sample, class counts are floors:

395 uncertain significance, 48 conflicting classifications of pathogenicity, 34 likely pathogenic, 24 benign/likely benign, 18 likely benign, 12 pathogenic/likely pathogenic, 10 pathogenic, 2 benign, 1 uncertain significance/vus-low

ClinVarVariant (HGVS)GeneClassificationReview
1215324NM_000789.4(ACE):c.2T>C (p.Met1Thr)ACEPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
18063NM_000789.4(ACE):c.798C>G (p.Tyr266Ter)ACEPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
235336NM_000789.4(ACE):c.1522C>T (p.Arg508Ter)ACEPathogeniccriteria provided, multiple submitters, no conflicts
2506013NM_000789.4(ACE):c.3409C>T (p.Gln1137Ter)ACEPathogeniccriteria provided, single submitter
2573840NM_000789.4(ACE):c.793C>T (p.Arg265Ter)ACEPathogeniccriteria provided, multiple submitters, no conflicts
2712424NM_000789.4(ACE):c.444_445insTTAGC (p.Arg149fs)ACEPathogeniccriteria provided, multiple submitters, no conflicts
3001305NM_000789.4(ACE):c.1186C>T (p.Gln396Ter)ACEPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
3341107NM_000789.4(ACE):c.21_30del (p.Arg8fs)ACEPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
4531674NM_000789.4(ACE):c.207G>A (p.Trp69Ter)ACEPathogeniccriteria provided, single submitter
50209NM_000789.4(ACE):c.2371C>T (p.Arg791Ter)ACEPathogeniccriteria provided, multiple submitters, no conflicts
827586NM_000789.4(ACE):c.1473_1475delinsA (p.Asp491fs)ACEPathogeniccriteria provided, multiple submitters, no conflicts
871758NM_000789.4(ACE):c.35TGC[1] (p.Leu13_Leu14del)ACEPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
429714NM_001384479.1(AGT):c.1060C>TAGTPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
429788NM_001384479.1(AGT):c.829+1G>TAGTPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1685512NM_000685.5(AGTR1):c.233del (p.Leu78fs)AGTR1Pathogeniccriteria provided, single submitter
2430252NM_000685.5(AGTR1):c.415C>T (p.Arg139Ter)AGTR1Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
50206NM_000685.5(AGTR1):c.251G>A (p.Trp84Ter)AGTR1Pathogeniccriteria provided, single submitter
13125NM_000537.4(REN):c.36GCT[3] (p.Leu16del)LOC107548112Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1940593NM_000789.4(ACE):c.232G>T (p.Glu78Ter)LOC130061383Pathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
1067090NM_000537.4(REN):c.249+1G>ARENPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
13123NM_000537.4(REN):c.145C>T (p.Arg49Ter)RENPathogenic/Likely pathogeniccriteria provided, multiple submitters, no conflicts
50210NM_000537.4(REN):c.127C>T (p.Arg43Ter)RENPathogeniccriteria provided, single submitter
1723253NM_000789.4(ACE):c.1511del (p.Pro504fs)ACELikely pathogeniccriteria provided, multiple submitters, no conflicts
1930250NM_000789.4(ACE):c.945+2T>GACELikely pathogeniccriteria provided, multiple submitters, no conflicts
2585611NM_000789.4(ACE):c.3G>T (p.Met1Ile)ACELikely pathogeniccriteria provided, single submitter
2627964NM_000789.4(ACE):c.973del (p.Val325fs)ACELikely pathogeniccriteria provided, single submitter
3234989NM_000789.4(ACE):c.1342+1G>TACELikely pathogeniccriteria provided, multiple submitters, no conflicts
3237477NM_000789.4(ACE):c.798C>A (p.Tyr266Ter)ACELikely pathogeniccriteria provided, single submitter
3391254NM_000789.4(ACE):c.2062C>T (p.Gln688Ter)ACELikely pathogeniccriteria provided, single submitter
3582403NM_000789.4(ACE):c.2T>A (p.Met1Lys)ACELikely pathogeniccriteria provided, single submitter

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 39 · Orphanet: 6 · 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.

GeneClassificationInheritanceDiseaseRecords
ACEStrongAutosomal recessiverenal tubular dysgenesis of genetic origin6
AGTStrongAutosomal recessiverenal tubular dysgenesis of genetic origin3
AGTR1StrongAutosomal recessiverenal tubular dysgenesis of genetic origin5
AGXTStrongAutosomal recessiverenal tubular dysgenesis of genetic origin9
KCTD11StrongAutosomal recessiverenal tubular dysgenesis of genetic origin8
RENStrongAutosomal recessiverenal tubular dysgenesis of genetic origin8

Orphanet rare-disease linkage (cohort genes)

GeneOrphanet IDRare disease
ACEOrphanet:97369Renal tubular dysgenesis of genetic origin
AGTOrphanet:97369Renal tubular dysgenesis of genetic origin
AGTR1Orphanet:97369Renal tubular dysgenesis of genetic origin
AGXTOrphanet:93598Primary hyperoxaluria type 1
RENOrphanet:217330REN-related autosomal dominant tubulointerstitial kidney disease
RENOrphanet:97369Renal tubular dysgenesis of genetic origin

Cohort genes → proteins

6 cohort genes, 6 distinct canonical proteins.

Evidence partition

SubsetGenes
multi_evidence6

Cohort genes (full)

SymbolHGNCEnsemblUniProtNameEvidence
KCTD11HGNC:21302ENSG00000213859Q693B1BTB/POZ domain-containing protein KCTD11gencc,clinvar
ACEHGNC:2707ENSG00000159640P12821Angiotensin-converting enzymegencc,clinvar
AGTHGNC:333ENSG00000135744P01019Angiotensinogengencc,clinvar
AGTR1HGNC:336ENSG00000144891P30556Type-1 angiotensin II receptorgencc,clinvar
AGXTHGNC:341ENSG00000172482P21549Alanine–glyoxylate aminotransferasegencc,clinvar
RENHGNC:9958ENSG00000143839P00797Reningencc,clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

SymbolProtein nameFunction (lead sentence)
KCTD11BTB/POZ domain-containing protein KCTD11Plays a role as a marker and a regulator of neuronal differentiation; Up-regulated by a variety of neurogenic signals, such as retinoic acid, epidermal growth factor/EGF and NGFB/nerve growth factor.
ACEAngiotensin-converting enzymeDipeptidyl carboxypeptidase that removes dipeptides from the C-terminus of a variety of circulating hormones, such as angiotensin I, bradykinin or enkephalins, thereby playing a key role in the regulation of blood pressure, electrolyte hom…
AGTAngiotensinogenEssential component of the renin-angiotensin system (RAS), a potent regulator of blood pressure, body fluid and electrolyte homeostasis.
AGTR1Type-1 angiotensin II receptorReceptor for angiotensin II, a vasoconstricting peptide, which acts as a key regulator of blood pressure and sodium retention by the kidney.
AGXTAlanine–glyoxylate aminotransferasePeroxisomal aminotransferase that catalyzes the transamination of glyoxylate to glycine and contributes to the glyoxylate detoxification.
RENReninRenin is a highly specific endopeptidase, whose only known function is to generate angiotensin I from angiotensinogen in the plasma, initiating a cascade of reactions that produce an elevation of blood pressure and increased sodium retenti…

Protein-family classification

Druggable: 4 · Difficult: 0 · Unknown: 2 · Druggable fraction: 0.67

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.

FamilyGenesFoldFDR
Protease212.2×0.042
GPCR14.0×0.452
Enzyme (other)12.0×0.543
Other/Unknown20.6×0.936

Per-gene assignment

SymbolFamilyDruggable?ECInterPro (top 3)
KCTD11Other/UnknownnoT1-type_BTB, SKP1/BTB/POZ_sf, KCTD11/21_C
ACEProteaseyes3.4.15.1Peptidase_M2
AGTOther/UnknownnoSerpin_fam, Angiotensinogen, Serpin_CS
AGTR1GPCRyesATII_AT1_rcpt, ATII_rcpt, GPCR_Rhodpsn
AGXTEnzyme (other)yes2.6.1.44Aminotrans_V_dom, PyrdxlP-dep_Trfase_major, PyrdxlP-dep_Trfase_small
RENProteaseyes3.4.23.15Aspartic_peptidase_A1, Aspartic_peptidase_AS, Aspartic_peptidase_N

Expression context

Cohort genes with no expression data: 0.

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

Breadth distribution (Bgee present_calls)

BucketGenes
narrow (1-5 tissues)0
moderate (6-20)0
broad (>20)6
unknown0

Top tissues across cohort

TissueCohort genes
liver2
right lobe of liver2
esophagus mucosa1
lower esophagus mucosa1
tibial nerve1
ileal mucosa1
left testis1
right testis1
lateral globus pallidus1
placenta1
skin of hip1
subcutaneous adipose tissue1
endometrium epithelium1
adult mammalian kidney1
decidua1
stromal cell of endometrium1

Per-gene tissue summary (top 30)

SymbolBgee breadthFANTOM5 breadthSCXATop tissues
KCTD11132ubiquitousmarkerlower esophagus mucosa, tibial nerve, esophagus mucosa
ACE177ubiquitousmarkerileal mucosa, right testis, left testis
AGT255broadmarkerright lobe of liver, liver, lateral globus pallidus
AGTR1224markerskin of hip, placenta, subcutaneous adipose tissue
AGXT125tissue_specificmarkerright lobe of liver, liver, endometrium epithelium
REN126tissue_specificmarkerdecidua, adult mammalian kidney, stromal cell of endometrium

Protein interactions among cohort

Intra-cohort edges: 6.

Hub genes (top 10 by interactor count)

SymbolInteractor count
AGT5,091
ACE3,659
REN3,244
AGTR12,651
AGXT2,648
KCTD11420

Intra-cohort edges

ABSources
ACEAGTbiogrid_interaction, string_interaction
ACEAGTR1string_interaction
ACERENstring_interaction
AGTAGTR1intact, string_interaction
AGTRENbiogrid_interaction, intact, string_interaction
AGTR1RENstring_interaction

Structural data

PDB: 5 · AlphaFold-only: 1 · No structure: 0

Cohort genes with PDB structures (top 30)

SymbolUniProtPDB entries
ACEP1282197
RENP0079791
AGTP0101922
AGXTP2154917
AGTR1P3055611

AlphaFold-only cohort genes (top 30 by pLDDT)

SymbolUniProtpLDDT
KCTD11Q693B185.00

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 23. Enrichment computed across 6 evidence-associated genes (5 with Reactome annotation).

Pathways by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 5 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

PathwayCohort genesFoldFDRSample cohort genes
Metabolism of Angiotensinogen to Angiotensins3380.7×8e-07ACE, AGT, REN
Peptide hormone metabolism2108.8×0.002ACE, AGT
Class A/1 (Rhodopsin-like receptors)229.7×0.010AGT, AGTR1
Peptide ligand-binding receptors229.7×0.010AGT, AGTR1
GPCR ligand binding225.7×0.011AGT, AGTR1
G alpha (q) signalling events222.9×0.011AGT, AGTR1
GPCR downstream signalling217.4×0.017AGT, AGTR1
Glyoxylate metabolism and glycine degradation1152.3×0.017AGXT
Signaling by GPCR216.0×0.017AGT, AGTR1
Protein localization138.1×0.060AGXT
Peroxisomal protein import134.6×0.060AGXT
Regulation of lipid metabolism by PPARalpha128.2×0.067AGT
Cargo recognition for clathrin-mediated endocytosis120.9×0.082AGTR1
PPARA activates gene expression118.9×0.082AGT
Clathrin-mediated endocytosis117.0×0.082AGTR1
Metabolism of proteins25.0×0.082ACE, AGT
Metabolism24.7×0.084AGT, AGXT
Metabolism of amino acids and derivatives113.5×0.092AGXT
Signal Transduction24.1×0.096AGT, AGTR1
G alpha (i) signalling events17.8×0.140AGT
Membrane Trafficking17.4×0.140AGTR1
Vesicle-mediated transport17.0×0.142AGTR1
Metabolism of lipids16.3×0.149AGT

GO biological processes by enrichment

Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 6 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.

GO termCohort genesFoldFDRSample cohort genes
renin-angiotensin regulation of aldosterone production32808.7×3e-09AGT, AGTR1, REN
angiotensin-activated signaling pathway3766.0×2e-07ACE, AGT, AGTR1
regulation of vasoconstriction3401.2×1e-06ACE, AGT, AGTR1
kidney development493.6×1e-06ACE, AGT, AGTR1, REN
regulation of renal output by angiotensin22808.7×2e-06ACE, AGT
maintenance of blood vessel diameter homeostasis by renin-angiotensin21872.4×6e-06AGT, AGTR1
regulation of renal sodium excretion21404.3×1e-05AGT, AGTR1
regulation of systemic arterial blood pressure by renin-angiotensin21123.5×1e-05ACE, AGTR1
regulation of blood pressure3110.9×2e-05ACE, AGT, REN
positive regulation of cholesterol metabolic process2702.2×3e-05AGT, AGTR1
amyloid-beta metabolic process2510.7×6e-05ACE, REN
angiotensin maturation2432.1×7e-05ACE, REN
low-density lipoprotein particle remodeling2351.1×1e-04AGT, AGTR1
positive regulation of macrophage derived foam cell differentiation2280.9×2e-04AGT, AGTR1
blood vessel diameter maintenance2208.1×3e-04ACE, AGTR1
positive regulation of reactive oxygen species metabolic process2170.2×4e-04AGT, AGTR1
blood vessel remodeling2127.7×6e-04ACE, AGT
regulation of cell growth273.9×0.002AGT, AGTR1
regulation of blood volume by renin-angiotensin12808.7×0.002AGT
mononuclear cell proliferation12808.7×0.002ACE
G protein-coupled receptor signaling pathway coupled to cGMP nucleotide second messenger11404.3×0.003AGT
regulation of angiotensin metabolic process11404.3×0.003ACE
response to cGMP11404.3×0.003REN
cell proliferation in bone marrow11404.3×0.003ACE
negative regulation of gap junction assembly11404.3×0.003ACE
male gonad development252.0×0.003ACE, REN
positive regulation of inflammatory response248.4×0.003AGT, AGTR1
phospholipase C-activating G protein-coupled receptor signaling pathway243.9×0.003AGT, AGTR1
substance P catabolic process1936.2×0.003ACE
obsolete glycine biosynthetic process, by transamination of glyoxylate1936.2×0.003AGXT

Therapeutics

Drug target analysis

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

Druggability breadth: 6 of 6 evidence-associated genes (100%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Genes with an approved drug

The molecule shown is one approved compound that hits the gene — not necessarily a drug of choice or one indicated for this disease.

SymbolExample approved molecule
ACETELMISARTAN
AGTR1IRBESARTAN
RENCAPTOPRIL

Top cohort targets by molecule count

SymbolMoleculesMax phase
AGTR1884
ACE314
REN134
KCTD1100
AGT00
AGXT00

Drugs targeting cohort genes (top 30)

MoleculeMax phaseTargets in cohort
TELMISARTAN4ACE, AGTR1
MOEXIPRIL4ACE
RAMIPRIL4ACE
LISINOPRIL ANHYDROUS4ACE
SITAGLIPTIN4ACE
TRANDOLAPRIL4ACE
CAPTOPRIL4ACE, REN
PERINDOPRIL4ACE
QUINAPRIL4ACE
LOSARTAN4ACE, AGTR1
FOSINOPRIL4ACE
IMIDAPRIL4ACE
ENALAPRILAT ANHYDROUS4ACE
ENALAPRIL4ACE
BENAZEPRIL4ACE
IRBESARTAN4AGTR1
SARALASIN4AGTR1
LOSARTAN POTASSIUM4AGTR1
CANDESARTAN CILEXETIL4AGTR1
CLOTRIMAZOLE4AGTR1
SIMVASTATIN4AGTR1
VALSARTAN4AGTR1
RIMONABANT4AGTR1
ARIPIPRAZOLE4AGTR1
PONATINIB4AGTR1
OXYMETHOLONE4AGTR1
OLMESARTAN MEDOXOMIL4AGTR1
NORGESTIMATE4AGTR1
ROCURONIUM4AGTR1
PYRVINIUM4AGTR1

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 3.

Cohort genes with ChEMBL bioactivity (full, sorted by assay count)

SymbolAssaysType breakdown
REN541Binding:472, Functional:68, ADMET:1
AGTR1421Binding:315, Functional:105, ADMET:1
ACE304Binding:288, Functional:8, ADMET:5, Unclassified:3
AGXT8Binding:8
AGT2Binding:2
KCTD111Binding:1

Cohort enzymes (BRENDA EC)

SymbolEC numbersNames
ACE3.4.15.1peptidyl-dipeptidase A
AGXT2.6.1.44, 2.6.1.51alanine-glyoxylate transaminase, serine-pyruvate transaminase
REN3.4.23.15renin

Cohort genes with high screening signal

≥100 ChEMBL assays — a studied-ness signal; see Therapeutics for approved-drug status.

SymbolChEMBL assays
ACE304
AGTR1421
REN541

Pharmacogenomics

Cohort genes with a PharmGKB record: 6; with CPIC/DPWG dosing guidelines: 0.

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

Chemical tractability of cohort targets

30 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.

CompoundMax phaseCohort target (bioactivity)
TELMISARTAN4ACE, AGTR1
MOEXIPRIL4ACE
RAMIPRIL4ACE
LISINOPRIL ANHYDROUS4ACE
SITAGLIPTIN4ACE
TRANDOLAPRIL4ACE
CAPTOPRIL4ACE, REN
PERINDOPRIL4ACE
QUINAPRIL4ACE
LOSARTAN4ACE, AGTR1
FOSINOPRIL4ACE
IMIDAPRIL4ACE
ENALAPRILAT ANHYDROUS4ACE
ENALAPRIL4ACE
BENAZEPRIL4ACE
IRBESARTAN4AGTR1
SARALASIN4AGTR1
LOSARTAN POTASSIUM4AGTR1
CANDESARTAN CILEXETIL4AGTR1
CLOTRIMAZOLE4AGTR1
SIMVASTATIN4AGTR1
VALSARTAN4AGTR1
RIMONABANT4AGTR1
ARIPIPRAZOLE4AGTR1
PONATINIB4AGTR1
OXYMETHOLONE4AGTR1
OLMESARTAN MEDOXOMIL4AGTR1
NORGESTIMATE4AGTR1
ROCURONIUM4AGTR1
PYRVINIUM4AGTR1

Druggability pyramid

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

TierDefinitionGenesSymbols
AApproved (phase 4 drug)3ACE, AGTR1, REN
BPhased (≥1) drug, not yet approved0
CDruggable family + PDB, no drug1AGXT
DDruggable family + AlphaFold only, no drug0
EDifficult family or no structure, no drug2KCTD11, AGT

Undrugged target profiles

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

SymbolChEMBL assaysDrugged partners (top 3)
AGT2AGTR1, ACE, REN
KCTD111
AGXT8

Clinical trials & evidence

Clinical trials

Clinical trials: 0.