Nephrotic syndrome, type 11

Summary

Nephrotic syndrome, type 11 (MONDO:0014752) is a disease caused by NUP107 (GenCC Strong), with 1 cohort gene.

At a glance

• Causal gene: NUP107 (GenCC Strong)
• Cohort genes: 1
• ClinVar variants: 16

Clinical features

No curated clinical features (Orphanet) for this disease.

Identifiers

Disease identifiers

Field	Value
Canonical name	nephrotic syndrome, type 11
Mondo ID	MONDO:0014752
OMIM	616730
DOID	DOID:0080385
UMLS	C4225228
MedGen	898622
GARD	0016155
Is cancer (heuristic)	no

Also known as: familial nephrotic syndrome caused by mutation in NUP107 · familial nephrotic syndrome caused by mutation in Nup107 · nephrotic syndrome, type 11 · nephrotic syndrome, type 11; NPHS11 · NPHS11 · NUP107 familial nephrotic syndrome · Nup107 familial nephrotic syndrome

Data availability: 16 ClinVar variants · 2 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 11

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 12, nephrotic syndrome, type 13, 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

16 retrieved; paginated sample, class counts are floors:

5 uncertain significance, 4 likely pathogenic, 3 benign, 3 pathogenic, 1 likely benign

ClinVar	Variant (HGVS)	Gene	Classification	Review
219127	NM_020401.4(NUP107):c.2492A>C (p.Asp831Ala)	NUP107	Pathogenic	criteria provided, single submitter
219128	NM_020401.4(NUP107):c.1079_1083del (p.Glu360fs)	NUP107	Pathogenic	no assertion criteria provided
219129	NM_020401.4(NUP107):c.969+1G>A	NUP107	Pathogenic	no assertion criteria provided
1685387	NM_020401.4(NUP107):c.2544_2555del (p.Leu848_Leu852delinsPhe)	NUP107	Likely pathogenic	criteria provided, single submitter
1687223	NM_020401.4(NUP107):c.580C>T (p.Arg194Ter)	NUP107	Likely pathogenic	criteria provided, single submitter
219130	NM_020401.4(NUP107):c.469G>T (p.Asp157Tyr)	NUP107	Likely pathogenic	criteria provided, single submitter
590324	NM_020401.4(NUP107):c.2666A>G (p.Tyr889Cys)	NUP107	Likely pathogenic	criteria provided, single submitter
1705532	NM_020401.4(NUP107):c.824_826del (p.Ser275del)	NUP107	Uncertain significance	criteria provided, single submitter
2681771	NM_020401.4(NUP107):c.1451_1453del (p.Gly484del)	NUP107	Uncertain significance	criteria provided, single submitter
2681772	NM_020401.4(NUP107):c.727A>G (p.Thr243Ala)	NUP107	Uncertain significance	criteria provided, single submitter
3377232	NM_020401.4(NUP107):c.100+1G>A	NUP107	Uncertain significance	criteria provided, single submitter
4293874	NM_020401.4(NUP107):c.2582T>G (p.Leu861Arg)	NUP107	Uncertain significance	criteria provided, single submitter
1261514	NM_020401.4(NUP107):c.1998+15G>T	NUP107	Benign	criteria provided, multiple submitters, no conflicts
1281812	NM_020401.4(NUP107):c.72G>A (p.Arg24=)	NUP107	Benign	criteria provided, multiple submitters, no conflicts
1286822	NM_020401.4(NUP107):c.1998+14G>T	NUP107	Benign	criteria provided, multiple submitters, no conflicts
774484	NM_020401.4(NUP107):c.353G>A (p.Arg118His)	NUP107	Likely benign	criteria provided, multiple submitters, no conflicts

Genes & proteins

Mendelian disease overlap and somatic drivers

GenCC: 11 · 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
NUP107	Strong	Autosomal recessive	nephrotic syndrome, type 11	11

Orphanet rare-disease linkage (cohort genes)

Gene	Orphanet ID	Rare disease
NUP107	Orphanet:2065	Galloway-Mowat syndrome
NUP107	Orphanet:243	46,XX gonadal dysgenesis
NUP107	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
NUP107	HGNC:29914	ENSG00000111581	P57740	Nuclear pore complex protein Nup107	gencc,clinvar

Cohort function summary

Lead sentence per gene, UniProt-curated.

Symbol	Protein name	Function (lead sentence)
NUP107	Nuclear pore complex protein Nup107	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)
NUP107	Other/Unknown	no		Nup84/Nup107

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
oocyte	1
secondary oocyte	1
ventricular zone	1

Per-gene tissue summary (top 30)

Symbol	Bgee breadth	FANTOM5 breadth	SCXA	Top tissues
NUP107	283	ubiquitous	marker	secondary oocyte, oocyte, ventricular zone

Protein interactions among cohort

Intra-cohort edges: 0.

Hub genes (top 10 by interactor count)

Symbol	Interactor count
NUP107	3,524

Structural data

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

Cohort genes with PDB structures (top 30)

Symbol	UniProt	PDB entries
NUP107	P57740	7

Function

Pathway analysis

Distinct Reactome pathways touched by cohort: 37. 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×	0.007	NUP107
IPs transport between nucleus and cytosol	1	380.7×	0.007	NUP107
IP3 and IP4 transport between cytosol and nucleus	1	380.7×	0.007	NUP107
IP6 and IP7 transport between cytosol and nucleus	1	380.7×	0.007	NUP107
Transport of Ribonucleoproteins into the Host Nucleus	1	356.9×	0.007	NUP107
Regulation of Glucokinase by Glucokinase Regulatory Protein	1	356.9×	0.007	NUP107
Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC)	1	356.9×	0.007	NUP107
NEP/NS2 Interacts with the Cellular Export Machinery	1	346.1×	0.007	NUP107
Nuclear import of Rev protein	1	335.9×	0.007	NUP107
Vpr-mediated nuclear import of PICs	1	335.9×	0.007	NUP107
Transport of the SLBP independent Mature mRNA	1	326.3×	0.007	NUP107
SUMOylation of SUMOylation proteins	1	326.3×	0.007	NUP107
Transport of the SLBP Dependant Mature mRNA	1	317.2×	0.007	NUP107
Rev-mediated nuclear export of HIV RNA	1	317.2×	0.007	NUP107
Nuclear Pore Complex (NPC) Disassembly	1	308.6×	0.007	NUP107
SUMOylation of ubiquitinylation proteins	1	292.8×	0.007	NUP107
NS1 Mediated Effects on Host Pathways	1	285.5×	0.007	NUP107
Transport of Mature mRNA Derived from an Intronless Transcript	1	271.9×	0.007	NUP107
Viral Messenger RNA Synthesis	1	259.6×	0.007	NUP107
SUMOylation of DNA replication proteins	1	248.3×	0.007	NUP107
SUMOylation of RNA binding proteins	1	237.9×	0.007	NUP107
snRNP Assembly	1	211.5×	0.008	NUP107
tRNA processing in the nucleus	1	196.9×	0.008	NUP107
SUMOylation of chromatin organization proteins	1	158.6×	0.009	NUP107
Transport of Mature mRNA derived from an Intron-Containing Transcript	1	152.3×	0.009	NUP107
ISG15 antiviral mechanism	1	150.3×	0.009	NUP107
SUMOylation of DNA damage response and repair proteins	1	146.4×	0.009	NUP107
Regulation of HSF1-mediated heat shock response	1	139.3×	0.009	NUP107
Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal	1	116.5×	0.011	NUP107
HCMV Late Events	1	98.5×	0.013	NUP107

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
post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery	1	5617.3×	0.001	NUP107
nephron development	1	1872.4×	0.001	NUP107
nuclear pore complex assembly	1	1685.2×	0.001	NUP107
female gonad development	1	802.5×	0.002	NUP107
nucleocytoplasmic transport	1	391.9×	0.004	NUP107
mRNA export from nucleus	1	295.6×	0.004	NUP107
protein import into nucleus	1	144.0×	0.007	NUP107

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
NUP107	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	NUP107

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)
NUP107	0	—

Clinical trials & evidence

Clinical trials

Clinical trials: 0.