Congenital anomalies of kidney and urinary tract 3
diseaseOn this page
Also known as CAKUT3
Summary
Congenital anomalies of kidney and urinary tract 3 (MONDO:0032646) is a disease with 1 cohort gene.
At a glance
- Cohort genes: 1
- ClinVar variants: 18
Clinical features
No curated clinical features (Orphanet) for this disease.
Identifiers
Disease identifiers
| Field | Value |
|---|---|
| Canonical name | congenital anomalies of kidney and urinary tract 3 |
| Mondo ID | MONDO:0032646 |
| OMIM | 618270 |
| UMLS | C4748921 |
| MedGen | 1648427 |
| GARD | 0025711 |
| Is cancer (heuristic) | no |
Also known as: CAKUT3
Data availability: 18 ClinVar variants · 1 GenCC gene-disease record.
Disease family
Classification path: disease › human disease › disease by developmental or physiological process › disorder of development or morphogenesis › developmental defect during embryogenesis › congenital anomaly of kidney and urinary tract › congenital anomalies of kidney and urinary tract 3
Related subtypes (2): congenital anomalies of kidney and urinary tract 1, congenital anomalies of kidney and urinary tract 2
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
18 retrieved; paginated sample, class counts are floors:
11 uncertain significance, 3 likely benign, 2 likely pathogenic, 1 benign, 1 pathogenic
| ClinVar | Variant (HGVS) | Gene | Classification | Review |
|---|---|---|---|---|
| 548653 | NM_003489.4(NRIP1):c.279del (p.Asp92_Trp93insTer) | NRIP1 | Pathogenic | no assertion criteria provided |
| 4533294 | NM_003489.4(NRIP1):c.2791A>T (p.Lys931Ter) | NRIP1 | Likely pathogenic | criteria provided, single submitter |
| 4812934 | NM_003489.4(NRIP1):c.3203T>C (p.Leu1068Pro) | NRIP1 | Likely pathogenic | no assertion criteria provided |
| 1339141 | NM_003489.4(NRIP1):c.2227G>A (p.Glu743Lys) | NRIP1 | Uncertain significance | criteria provided, single submitter |
| 1339181 | NM_003489.4(NRIP1):c.1868C>T (p.Ala623Val) | NRIP1 | Uncertain significance | criteria provided, single submitter |
| 1723300 | NM_003489.4(NRIP1):c.3465_3468del (p.Lys1155fs) | NRIP1 | Uncertain significance | criteria provided, multiple submitters, no conflicts |
| 2226213 | NM_003489.4(NRIP1):c.860C>T (p.Thr287Met) | NRIP1 | Uncertain significance | criteria provided, multiple submitters, no conflicts |
| 2394795 | NM_003489.4(NRIP1):c.3364A>G (p.Arg1122Gly) | NRIP1 | Uncertain significance | criteria provided, multiple submitters, no conflicts |
| 3236105 | NM_003489.4(NRIP1):c.739G>A (p.Val247Met) | NRIP1 | Uncertain significance | criteria provided, single submitter |
| 3367024 | NM_003489.4(NRIP1):c.3439C>G (p.Leu1147Val) | NRIP1 | Uncertain significance | criteria provided, single submitter |
| 3390953 | NM_003489.4(NRIP1):c.1627_1628delinsTT (p.Pro543Phe) | NRIP1 | Uncertain significance | criteria provided, single submitter |
| 3891858 | NM_003489.4(NRIP1):c.3235G>C (p.Val1079Leu) | NRIP1 | Uncertain significance | criteria provided, single submitter |
| 4277854 | NM_003489.4(NRIP1):c.2837_2838del (p.Val946fs) | NRIP1 | Uncertain significance | criteria provided, single submitter |
| 992908 | NM_003489.4(NRIP1):c.1660C>T (p.Pro554Ser) | NRIP1 | Uncertain significance | criteria provided, single submitter |
| 1326992 | NM_003489.4(NRIP1):c.225G>A (p.Gly75=) | NRIP1 | Benign | criteria provided, multiple submitters, no conflicts |
| 2164085 | NM_003489.4(NRIP1):c.2038G>A (p.Ala680Thr) | NRIP1 | Likely benign | criteria provided, multiple submitters, no conflicts |
| 2706648 | NM_003489.4(NRIP1):c.2840G>A (p.Arg947Gln) | NRIP1 | Likely benign | criteria provided, multiple submitters, no conflicts |
| 734220 | NM_003489.4(NRIP1):c.3455C>T (p.Thr1152Met) | NRIP1 | Likely benign | criteria provided, multiple submitters, no conflicts |
Genes & proteins
Mendelian disease overlap and somatic drivers
GenCC: 1 · Orphanet: 0 · 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 |
|---|---|---|---|---|
| NRIP1 | Limited | Autosomal dominant | congenital anomalies of kidney and urinary tract 3 |
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 |
|---|---|---|---|---|---|
| NRIP1 | HGNC:8001 | ENSG00000180530 | P48552 | Nuclear receptor-interacting protein 1 | gencc,clinvar |
Cohort function summary
Lead sentence per gene, UniProt-curated.
| Symbol | Protein name | Function (lead sentence) |
|---|---|---|
| NRIP1 | Nuclear receptor-interacting protein 1 | Modulates transcriptional activation by steroid receptors such as NR3C1, NR3C2 and ESR1. |
Protein-family classification
Druggable: 0 · Difficult: 0 · Unknown: 1 · 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 |
|---|---|---|---|
| Other/Unknown | 1 | 1.8× | 0.558 |
Per-gene assignment
| Symbol | Family | Druggable? | EC | InterPro (top 3) |
|---|---|---|---|---|
| NRIP1 | Other/Unknown | no | NRIP1, NRIP1_RD1, NRIP1_RD2 |
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 |
|---|---|
| caput epididymis | 1 |
| corpus epididymis | 1 |
| jejunal mucosa | 1 |
Per-gene tissue summary (top 30)
| Symbol | Bgee breadth | FANTOM5 breadth | SCXA | Top tissues |
|---|---|---|---|---|
| NRIP1 | 294 | ubiquitous | marker | corpus epididymis, caput epididymis, jejunal mucosa |
Protein interactions among cohort
Intra-cohort edges: 0.
Hub genes (top 10 by interactor count)
| Symbol | Interactor count |
|---|---|
| NRIP1 | 1,681 |
Structural data
PDB: 1 · AlphaFold-only: 0 · No structure: 0
Cohort genes with PDB structures (top 30)
| Symbol | UniProt | PDB entries |
|---|---|---|
| NRIP1 | P48552 | 17 |
Function
Pathway analysis
Distinct Reactome pathways touched by cohort: 7. Enrichment computed across 1 evidence-associated genes (1 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 1 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.
| Pathway | Cohort genes | Fold | FDR | Sample cohort genes |
|---|---|---|---|---|
| NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis | 1 | 2284.0× | 0.003 | NRIP1 |
| NR1H2 & NR1H3 regulate gene expression linked to lipogenesis | 1 | 1142.0× | 0.003 | NRIP1 |
| RORA,B,C and NR1D1 (REV-ERBA) regulate gene expression | 1 | 407.9× | 0.005 | NRIP1 |
| Expression of BMAL (ARNTL), CLOCK, and NPAS2 | 1 | 292.8× | 0.005 | NRIP1 |
| SUMOylation of transcription cofactors | 1 | 243.0× | 0.005 | NRIP1 |
| Heme signaling | 1 | 215.5× | 0.005 | NRIP1 |
| Estrogen-dependent gene expression | 1 | 75.6× | 0.013 | NRIP1 |
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 |
|---|---|---|---|---|
| ovarian follicle rupture | 1 | 16852.0× | 4e-04 | NRIP1 |
| lipid storage | 1 | 543.6× | 0.006 | NRIP1 |
| cellular response to estradiol stimulus | 1 | 411.0× | 0.006 | NRIP1 |
| circadian rhythm | 1 | 244.2× | 0.006 | NRIP1 |
| circadian regulation of gene expression | 1 | 234.1× | 0.006 | NRIP1 |
| negative regulation of transcription by RNA polymerase II | 1 | 17.7× | 0.066 | NRIP1 |
| positive regulation of transcription by RNA polymerase II | 1 | 14.9× | 0.067 | NRIP1 |
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 |
|---|---|---|
| NRIP1 | 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 | NRIP1 |
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) |
|---|---|---|
| NRIP1 | 0 | — |
Clinical trials & evidence
Clinical trials
Clinical trials: 0.
Related Atlas pages
- Cohort genes: NRIP1