Nephrotic syndrome, type 13

Summary

Nephrotic syndrome, type 13 (MONDO:0014818) is a disease caused by NUP205 (GenCC Strong), with 1 cohort gene.

At a glance

• Causal gene: NUP205 (GenCC Strong)
• Cohort genes: 1
• ClinVar variants: 15

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	nephrotic syndrome, type 13
Mondo ID	MONDO:0014818
OMIM	616893
DOID	DOID:0080381
UMLS	C4225165
MedGen	900240
GARD	0016167
Is cancer (heuristic)	no

Also known as: familial nephrotic syndrome caused by mutation in NUP205 · nephrotic syndrome, type 13 · nephrotic syndrome, type 13; NPHS13 · NPHS13 · NUP205 familial nephrotic syndrome

Data availability: 15 ClinVar variants · 3 GenCC gene-disease records.

Disease family

Classification path: disease › human disease › disease by body system or component › syndromic disease › nephrotic syndrome › familial nephrotic syndrome › familial idiopathic steroid-resistant nephrotic syndrome › nephrotic syndrome, type 13

Related subtypes (13): nephrotic syndrome, type 2, focal segmental glomerulosclerosis 1, nephrotic syndrome, type 3, nephrotic syndrome, type 6, familial steroid-resistant nephrotic syndrome with sensorineural deafness, nephrotic syndrome, type 8, nephrotic syndrome, type 9, nephrotic syndrome, type 10, nephrotic syndrome, type 11, nephrotic syndrome, type 12, familial idiopathic steroid-resistant nephrotic syndrome with diffuse mesangial proliferation, familial idiopathic steroid-resistant nephrotic syndrome with minimal changes, familial idiopathic steroid-resistant nephrotic syndrome with diffuse mesangial sclerosis

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

15 retrieved; paginated sample, class counts are floors:

6 uncertain significance, 5 benign, 1 pathogenic, 1 conflicting classifications of pathogenicity, 1 benign/likely benign, 1 likely pathogenic

ClinVar	Variant (HGVS)	Gene	Classification	Review
224969	NM_015135.3(NUP205):c.5984T>C (p.Phe1995Ser)	NUP205	Pathogenic	no assertion criteria provided
807642	NM_015135.3(NUP205):c.3329T>C (p.Leu1110Pro)	NUP205	Likely pathogenic	criteria provided, single submitter
2756249	NM_015135.3(NUP205):c.490C>T (p.Pro164Ser)	NUP205	Conflicting classifications of pathogenicity	criteria provided, conflicting classifications
1414591	NM_015135.3(NUP205):c.2961C>G (p.Ile987Met)	NUP205	Uncertain significance	criteria provided, multiple submitters, no conflicts
2434468	NM_015135.3(NUP205):c.5246T>C (p.Ile1749Thr)	NUP205	Uncertain significance	criteria provided, multiple submitters, no conflicts
2434469	NM_015135.3(NUP205):c.821C>T (p.Ala274Val)	NUP205	Uncertain significance	criteria provided, multiple submitters, no conflicts
2434470	NM_015135.3(NUP205):c.5789T>A (p.Leu1930Ter)	NUP205	Uncertain significance	criteria provided, single submitter
2434471	NM_015135.3(NUP205):c.2453T>C (p.Leu818Pro)	NUP205	Uncertain significance	criteria provided, multiple submitters, no conflicts
2442397	NM_015135.3(NUP205):c.2068G>A (p.Glu690Lys)	NUP205	Uncertain significance	criteria provided, single submitter
1224632	NM_015135.3(NUP205):c.1851A>C (p.Ala617=)	NUP205	Benign	criteria provided, multiple submitters, no conflicts
1263165	NM_015135.3(NUP205):c.5559+4C>T	NUP205	Benign	criteria provided, multiple submitters, no conflicts
1264849	NM_015135.3(NUP205):c.649-11T>C	NUP205	Benign	criteria provided, multiple submitters, no conflicts
1278454	NM_015135.3(NUP205):c.4793+11G>A	NUP205	Benign	criteria provided, multiple submitters, no conflicts
1327023	NM_015135.3(NUP205):c.4066G>C (p.Glu1356Gln)	NUP205	Benign	criteria provided, multiple submitters, no conflicts
710438	NM_015135.3(NUP205):c.4425C>T (p.Ala1475=)	NUP205	Benign/Likely benign	criteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 4 · Orphanet: 1 · 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
NUP205	Strong	Autosomal recessive	nephrotic syndrome, type 13	4

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
NUP205	Orphanet:656	Hereditary steroid-resistant nephrotic 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
NUP205	HGNC:18658	ENSG00000155561	Q92621	Nuclear pore complex protein Nup205	gencc,clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
NUP205	Nuclear pore complex protein Nup205	Plays a role in the nuclear pore complex (NPC) assembly and/or maintenance.

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)
NUP205	Other/Unknown	no		Nup186/Nup192/Nup205

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
embryo	1
ganglionic eminence	1
ventricular zone	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
NUP205	265	ubiquitous	marker	ventricular zone, ganglionic eminence, embryo

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
NUP205	2,881

Structural data

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

Cohort genes with PDB structures (top 30)

Symbol	UniProt	PDB entries
NUP205	Q92621	5

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 31. 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
Postmitotic nuclear pore complex (NPC) reformation	1	407.9×	0.006	NUP205
IPs transport between nucleus and cytosol	1	380.7×	0.006	NUP205
IP3 and IP4 transport between cytosol and nucleus	1	380.7×	0.006	NUP205
IP6 and IP7 transport between cytosol and nucleus	1	380.7×	0.006	NUP205
Transport of Ribonucleoproteins into the Host Nucleus	1	356.9×	0.006	NUP205
Regulation of Glucokinase by Glucokinase Regulatory Protein	1	356.9×	0.006	NUP205
Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC)	1	356.9×	0.006	NUP205
NEP/NS2 Interacts with the Cellular Export Machinery	1	346.1×	0.006	NUP205
Nuclear import of Rev protein	1	335.9×	0.006	NUP205
Vpr-mediated nuclear import of PICs	1	335.9×	0.006	NUP205
Transport of the SLBP independent Mature mRNA	1	326.3×	0.006	NUP205
SUMOylation of SUMOylation proteins	1	326.3×	0.006	NUP205
Transport of the SLBP Dependant Mature mRNA	1	317.2×	0.006	NUP205
Rev-mediated nuclear export of HIV RNA	1	317.2×	0.006	NUP205
Nuclear Pore Complex (NPC) Disassembly	1	308.6×	0.006	NUP205
SUMOylation of ubiquitinylation proteins	1	292.8×	0.006	NUP205
NS1 Mediated Effects on Host Pathways	1	285.5×	0.006	NUP205
Transport of Mature mRNA Derived from an Intronless Transcript	1	271.9×	0.006	NUP205
Viral Messenger RNA Synthesis	1	259.6×	0.006	NUP205
SUMOylation of DNA replication proteins	1	248.3×	0.006	NUP205
SUMOylation of RNA binding proteins	1	237.9×	0.006	NUP205
snRNP Assembly	1	211.5×	0.007	NUP205
tRNA processing in the nucleus	1	196.9×	0.007	NUP205
SUMOylation of chromatin organization proteins	1	158.6×	0.008	NUP205
Transport of Mature mRNA derived from an Intron-Containing Transcript	1	152.3×	0.008	NUP205
ISG15 antiviral mechanism	1	150.3×	0.008	NUP205
SUMOylation of DNA damage response and repair proteins	1	146.4×	0.008	NUP205
Regulation of HSF1-mediated heat shock response	1	139.3×	0.008	NUP205
HCMV Late Events	1	98.5×	0.011	NUP205
SARS-CoV-2 activates/modulates innate and adaptive immune responses	1	89.2×	0.012	NUP205

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
nuclear pore organization	1	2106.5×	0.001	NUP205
nuclear pore complex assembly	1	1685.2×	0.001	NUP205
nucleocytoplasmic transport	1	391.9×	0.004	NUP205
mRNA transport	1	263.3×	0.005	NUP205
protein transport	1	43.9×	0.023	NUP205

Therapeutics

Drug target analysis

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

Druggability breadth: 1 of 1 evidence-associated genes (100%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).

Top cohort targets by molecule count

Symbol	Molecules	Max phase
NUP205	1	2

Drugs targeting cohort genes (top 30)

Molecule	Max phase	Targets in cohort
MOLIBRESIB	2	NUP205

Bioactivity and enzyme data

Enzyme cohort genes (≥1 EC): 0.

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

Symbol	Assays	Type breakdown
NUP205	7	Binding:7

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

1 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.

Compound	Max phase	Cohort target (bioactivity)
MOLIBRESIB	2	NUP205

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	1	NUP205
C	Druggable family + PDB, no drug	0
D	Druggable family + AlphaFold only, no drug	0
E	Difficult family or no structure, no drug	0

Undrugged target profiles

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

Clinical trials & evidence

Clinical trials

Clinical trials: 0.