GeneBe

NUP107

protein-coding

nucleoporin 107, the group of Nucleoporins

Gene summary

This gene encodes a member of the nucleoporin family. The protein is localized to the nuclear rim and is an essential component of the nuclear pore complex (NPC). All molecules entering or leaving the nucleus either diffuse through or are actively transported by the NPC. Alternate transcriptional splice variants of this gene have been observed but have not been thoroughly characterized. [provided by RefSeq, Jul 2008]

MANE transcript

NM_020401.4

Inheritance

AD, AR

ClinVar variants

P:27U:183B:64

Top phenotype

Nephrotic syndrome, type 11; Ovarian dysgenesis 6; Galloway-Mowat syndrome 7

gnomAD constraint

pLI —, LoF o/e 0.41

Max pathogenic AF

—

Genomic locus

chr12:68,686,951-68,745,809

External References & Databases

Ensembl (ENSG00000111581)NCBI Gene (57122)OMIM (607617)HGNC:29914GenCCUniProt (P57740)AlphaFoldClinVar (NUP107)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~58.9 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

familial idiopathic steroid-resistant nephrotic syndromeSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0019006

Submitter: Orphanet

nephrotic syndrome, type 11STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0014752

Submitter: Labcorp Genetics (formerly Invitae)

Galloway-Mowat syndrome 7STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0032692

Submitter: Labcorp Genetics (formerly Invitae)

ovarian dysgenesis 6LIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0054850

Submitter: Ambry Genetics

Galloway-Mowat syndrome 7LIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0032692

Submitter: Ambry Genetics

ovarian dysgenesis 6STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0054850

Submitter: Labcorp Genetics (formerly Invitae)

46 XX gonadal dysgenesisSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0009299

Submitter: Orphanet

nephrotic syndrome, type 11MODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0014752

Submitter: Ambry Genetics

Galloway-Mowat syndromeSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0009627

Submitter: Orphanet

Galloway-Mowat syndrome 7STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0032692

Submitter: G2P

Galloway-Mowat syndrome 7STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0032692

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Nephrotic syndrome, type 11; Ovarian dysgenesis 6; Galloway-Mowat syndrome 7AR

Manifestation: Craniofacial; Endocrine; Musculoskeletal; Neurologic; Obstetric; 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: In Nephrotic syndrome and Galloway-Mowat syndrome, renal transplantation has been described; In Ovarian dysgenesis, to induce/maintain secondary sex characteristics, specific interventions (eg, medical hormonal treatment) may be necessary

Refs: 25558065; 26411495; 26485283; 28117080; 28280135; 30179222Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NUP107 variants in ClinVar

13 Conditions Cataloged
not providedTotal: 213
Inborn genetic diseasesTotal: 119
NUP107-related disorderTotal: 32
not specifiedTotal: 30
Nephrotic syndrome, type 11Total: 16
Galloway-Mowat syndrome 7Total: 10
Ovarian dysgenesis 6Total: 7
Light complexionTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020401.4. 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
7
clinvar
53
clinvar
1
clinvar
 61
missense
3
clinvar
4
clinvar
161
clinvar
10
clinvar
 178
nonsense
6
clinvar
4
clinvar
2
clinvar
 12
start loss
0
frameshift
1
clinvar
3
clinvar
3
clinvar
 7
splice donor/acceptor (+/-2bp)
1
clinvar
5
clinvar
10
clinvar
 16
Total1116183631274

Highest pathogenic variant AF is 0.00009890483

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 64 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_020401.4RefSeqNP_065134.128MANE Select
ENST00000229179.9EnsemblENSP00000229179.428MANE Select
NM_001330192.2RefSeqNP_001317121.126Standard
ENST00000378905.6EnsemblENSP00000368185.221Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
nup107Danio rerio

Structure: glomerular capillary

Quality: collapsed

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • RNA transport - Homo sapiens (human)
  • Gastric Cancer Network 1
  • tRNA processing
  • Disease
  • Signal Transduction

Biological Process

  • posttranscriptional tethering of RNA polymerase II gene DNA at nuclear periphery
  • mRNA export from nucleus
  • protein import into nucleus
  • female gonad development
  • viral process

Molecular Function

  • protein binding
  • structural constituent of nuclear pore

Cellular Component

  • kinetochore
  • condensed chromosome kinetochore
  • nuclear envelope
  • nuclear pore
  • cytosol

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000229179
Coding exons
28
Length
56272
Individuals with no LoFs
125659
Homozygous LoFs
0
Heterozygous LoFs
88
Defined
125747
p
0.000350
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense1.893734900.7600.00002576080
Missense (PolyPhen)122171.010.713412203
Synonymous0.9131491640.9090.000008231681
Loss of Function4.342663.30.4110.00000348714

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000250.00025rare
Latino/Admixed American0.000150.00014rare
Ashkenazi Jewish00.0absent
East Asian0.000630.00060rare
Finnish0.000280.00028rare
European (Non-Finnish)0.000430.00040rare
South Asian0.000540.00049rare
Other0.000160.00016rare

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Plays a role in the nuclear pore complex (NPC) assembly and/or maintenance (PubMed:12552102, PubMed:15229283). Required for the assembly of peripheral proteins into the NPC (PubMed:15229283, PubMed:12552102). May anchor NUP62 to the NPC (PubMed:15229283). {ECO:0000269|PubMed:12552102, ECO:0000269|PubMed:15229283}.;

Recessive Scores

pRec
0.155

Intolerance Scores

LoFtool
0.177
RVIS EVS
-0.55
RVIS percentile EVS
19.86

Essentials

Essential (CRISPR)
E
Essential (CRISPR2)
E
Essential (gene trap)
E
Indispensability pred.
E
Indispensability score
0.992

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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