NUP85
protein-codingnucleoporin 85, the group of Nucleoporins
Gene summary
This gene encodes a protein component of the Nup107-160 subunit of the nuclear pore complex. Nuclear pore complexes are embedded in the nuclear envelope and promote bidirectional transport of macromolecules between the cytoplasm and nucleus. The encoded protein can also bind to the C-terminus of chemokine (C-C motif) receptor 2 (CCR2) and promote chemotaxis of monocytes, thereby participating in the inflammatory response. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2014]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~30.1 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0032580
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0032580
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0032580
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: Unknown
Disease ID:MONDO:0007661
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0019006
Submitter: Orphanet
Clinical Genomic Database (CGD)
Manifestation: Musculoskeletal; 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
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to NUP85 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_024844.5. 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.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 3 | 41 | 3 | 47 | ||
| missense | 3 | 108 | 6 | 4 | 121 | |
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 3 | 4 | |||
| Total | 1 | 3 | 115 | 47 | 7 | 173 |
Highest pathogenic variant AF is 0.000035318088
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_079120.1 | 19 | MANE Select | |
| Ensembl | ENSP00000245544.4 | 19 | MANE Select | |
| RefSeq | NP_001290205.1 | 17 | Standard | |
| RefSeq | NP_001317401.1 | 18 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- RNA transport - Homo sapiens (human)
- Integrated Breast Cancer Pathway
- tRNA processing
- Disease
- Signal Transduction
Biological Process
- mRNA export from nucleus
- protein import into nucleus
- viral process
- lamellipodium assembly
- positive regulation of transcription, DNA-templated
Molecular Function
- protein binding
- structural constituent of nuclear pore
Cellular Component
- kinetochore
- condensed chromosome kinetochore
- nucleus
- nuclear envelope
- spindle
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000245544
- Coding exons
- 19
- Length
- 30100
- Individuals with no LoFs
- 125739
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 7
- Defined
- 125746
- p
- 0.0000278
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.755 | 336 | 377 | 0.891 | 0.0000222 | 4291 |
| Missense (PolyPhen) | 77 | 94.049 | 0.81872 | 1142 | ||
| Synonymous | -0.247 | 149 | 145 | 1.03 | 0.00000868 | 1251 |
| Loss of Function | 5.82 | 2 | 43.4 | 0.0461 | 0.00000242 | 455 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000058 | 0.000058 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000026 | 0.000026 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Essential component of the nuclear pore complex (NPC) that seems to be required for NPC assembly and maintenance (PubMed:12718872). As part of the NPC Nup107-160 subcomplex plays a role in RNA export and in tethering NUP96/Nup98 and NUP153 to the nucleus (PubMed:12718872). The Nup107-160 complex seems to be required for spindle assembly during mitosis (PubMed:16807356). NUP85 is required for membrane clustering of CCL2-activated CCR2 (PubMed:15995708). Seems to be involved in CCR2-mediated chemotaxis of monocytes and may link activated CCR2 to the phosphatidyl-inositol 3-kinase-Rac-lammellipodium protrusion cascade (PubMed:15995708). {ECO:0000269|PubMed:12718872, ECO:0000269|PubMed:15995708, ECO:0000269|PubMed:16807356}.;
Recessive Scores
- pRec
- 0.0946
Intolerance Scores
- LoFtool
- 0.0792
- RVIS EVS
- -0.93
- RVIS percentile EVS
- 9.61
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.862
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |