GeneBe

NUP205

protein-coding

nucleoporin 205, the group of Nucleoporins|Armadillo like helical domain containing

Gene summary

This gene encodes a nucleoporin, which is a subunit of the nuclear pore complex that functions in active transport of proteins, RNAs and ribonucleoprotein particles between the nucleus and cytoplasm. Mutations in this gene are associated with steroid-resistant nephrotic syndrome. [provided by RefSeq, Jul 2016]

Previous symbols:
  • C7orf14

MANE transcript

NM_015135.3

Inheritance

AR, AD

ClinVar variants

P:2U:311B:145

Top phenotype

Nephrotic syndrome, type 13

gnomAD constraint

pLI —, LoF o/e 0.16

Max pathogenic AF

—

Genomic locus

chr7:135,557,917-135,648,757

External References & Databases

Ensembl (ENSG00000155561)NCBI Gene (23165)OMIM (614352)HGNC:18658GenCCUniProt (Q92621)AlphaFoldClinVar (NUP205)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~90.8 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

nephrotic syndrome, type 13LIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0014818

Submitter: ClinGen

NUP205 was first reported in relation to autosomal recessive nephrotic syndrome 13 in 2016. (Braun et al., PMID: 26878725). Nucleoporins are essential components of the nuclear pore complex (NPC)1. Only a few diseases have been attributed to NPC dysfunction (Braun et al., PMID: 26878725)At least one pathogenic missense variant has been reported in humans. The p.Phe1995Ser was seen in two siblings with unrelated parents. In vitro functional expression studies showed that the mutation abrogated the interaction of NUP205 with NUP93 (PMID: 26878725) In summary, there is limited evidence to support this gene-disease relationship. Although more evidence is needed to support a causal role, no convincing evidence has emerged that contradicts the gene-disease relationship.This classification was approved by the ClinGen Glomerulopathy GCEP on the meeting September 27th 2022 (SOP Version 9)

nephrotic syndrome, type 13STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0014818

Submitter: Labcorp Genetics (formerly Invitae)

nephrotic syndrome, type 13LIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0014818

Submitter: PanelApp Australia

nephrotic syndrome, type 13LIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0014818

Submitter: Ambry Genetics

familial idiopathic steroid-resistant nephrotic syndromeSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0019006

Submitter: Orphanet

Clinical Genomic Database (CGD)

Nephrotic syndrome, type 13AR

Manifestation: Renal

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Comments: Renal transplantation has been described

Refs: 26878725Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NUP205 variants in ClinVar

6 Conditions Cataloged
not providedTotal: 318
not specifiedTotal: 262
NUP205-related disorderTotal: 43
Nephrotic syndrome, type 13Total: 11
Marfanoid habitus and intellectual disabilityTotal: 2
NUP205-related disordersTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015135.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
3
clinvar
116
clinvar
6
clinvar
 125
missense
2
clinvar
293
clinvar
22
clinvar
1
clinvar
 318
nonsense
3
clinvar
 3
start loss
0
frameshift
1
clinvar
 1
splice donor/acceptor (+/-2bp)
11
clinvar
 11
Total023111387458

Highest pathogenic variant AF is 0.0000061928454

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 41 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_015135.3RefSeqNP_055950.243MANE Select
ENST00000285968.11EnsemblENSP00000285968.643MANE Select
NM_001329434.2RefSeqNP_001316363.236Standard
ENST00000463247.1EnsemblENSP00000475539.13Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
nup205Danio rerio

Structure: trunk

Quality: curved dorsal

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • RNA transport - Homo sapiens (human)
  • tRNA processing
  • Disease
  • Gene expression (Transcription)
  • Regulation of HSF1-mediated heat shock response

Biological Process

  • mRNA export from nucleus
  • nucleocytoplasmic transport
  • nuclear pore organization
  • viral process
  • nuclear pore complex assembly

Molecular Function

  • protein binding
  • structural constituent of nuclear pore

Cellular Component

  • nuclear envelope
  • nuclear pore
  • membrane
  • nuclear membrane
  • nuclear periphery

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000285968
Coding exons
43
Length
90839
Individuals with no LoFs
125717
Homozygous LoFs
0
Heterozygous LoFs
31
Defined
125748
p
0.000123
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense1.359551.08e+30.8840.000057813096
Missense (PolyPhen)284349.380.812884343
Synonymous-0.4423933821.030.00001913912
Loss of Function8.37181150.1570.000006161321

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000250.00025rare
Latino/Admixed American0.000180.00017rare
Ashkenazi Jewish0.000200.00020rare
East Asian0.0000540.000054rare
Finnish0.0000930.000092rare
European (Non-Finnish)0.000130.00013rare
South Asian0.0000330.000033rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Plays a role in the nuclear pore complex (NPC) assembly and/or maintenance (PubMed:9348540). May anchor NUP62 and other nucleoporins, but not NUP153 and TPR, to the NPC (PubMed:15229283). {ECO:0000269|PubMed:15229283, ECO:0000269|PubMed:9348540}.;
Disease
DISEASE: Nephrotic syndrome 13 (NPHS13) [MIM:616893]: A form of nephrotic syndrome, a renal disease clinically characterized by severe proteinuria, resulting in complications such as hypoalbuminemia, hyperlipidemia and edema. Kidney biopsies show non-specific histologic changes such as focal segmental glomerulosclerosis and diffuse mesangial proliferation. Some affected individuals have an inherited steroid-resistant form and progress to end-stage renal failure. {ECO:0000269|PubMed:26878725}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec
0.122

Intolerance Scores

LoFtool
0.502
RVIS EVS
-0.96
RVIS percentile EVS
9.01

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
E
Essential (gene trap)
E
Indispensability pred.
E
Indispensability score
0.898

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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