GeneBe

NUP214

protein-coding

nucleoporin 214, the group of Nucleoporins

Gene summary

The nuclear pore complex is a massive structure that extends across the nuclear envelope, forming a gateway that regulates the flow of macromolecules between the nucleus and the cytoplasm. Nucleoporins are the main components of the nuclear pore complex in eukaryotic cells. This gene is a member of the FG-repeat-containing nucleoporins. The protein encoded by this gene is localized to the cytoplasmic face of the nuclear pore complex where it is required for proper cell cycle progression and nucleocytoplasmic transport. The 3' portion of this gene forms a fusion gene with the DEK gene on chromosome 6 in a t(6,9) translocation associated with acute myeloid leukemia and myelodysplastic syndrome. Alternative splicing of this gene results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2015]

MANE transcript

NM_005085.4

Inheritance

AR

ClinVar variants

P:9U:373B:89

Top phenotype

Encephalopathy, acute, infection-induced, suseptibility to, 9

gnomAD constraint

pLI —, LoF o/e 0.24

Max pathogenic AF

—

Genomic locus

chr9:131,125,573-131,234,663

External References & Databases

Ensembl (ENSG00000126883)NCBI Gene (8021)OMIM (114350)HGNC:8064GenCCUniProt (P35658)AlphaFoldClinVar (NUP214)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~109.1 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

encephalopathy, acute, infection-induced, susceptibility to, 9STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0032742

Submitter: G2P

encephalopathy, acute, infection-induced, susceptibility to, 9STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0032742

Submitter: Labcorp Genetics (formerly Invitae)

encephalopathy, acute, infection-induced, susceptibility to, 9LIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0032742

Submitter: Ambry Genetics

encephalopathy, acute, infection-induced, susceptibility to, 9STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0032742

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Encephalopathy, acute, infection-induced, suseptibility to, 9AR

Manifestation: Neurologic

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

Refs: 30758658; 31178128Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to NUP214 variants in ClinVar

14 Conditions Cataloged
not specifiedTotal: 380
not providedTotal: 97
Encephalopathy, acute, infection-induced, susceptibility to, 9Total: 20
NUP214-related disorderTotal: 12
Acute myeloid leukemiaTotal: 5
Acute lymphoid leukemiaTotal: 4
NUP14 Related DisordersTotal: 2
Progressive microcephalyTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005085.4. 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
5
clinvar
51
clinvar
2
clinvar
 58
missense
3
clinvar
356
clinvar
32
clinvar
3
clinvar
 394
nonsense
1
clinvar
2
clinvar
 3
start loss
0
frameshift
2
clinvar
3
clinvar
2
clinvar
 7
splice donor/acceptor (+/-2bp)
8
clinvar
1
clinvar
 9
Total27373845471

Highest pathogenic variant AF is 0.00004337255

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 57 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_005085.4RefSeqNP_005076.336MANE Select
ENST00000359428.10EnsemblENSP00000352400.536MANE Select
NM_001318324.2RefSeqNP_001305253.136Standard
NM_001318325.2RefSeqNP_001305254.111Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • RNA transport - Homo sapiens (human)
  • Epstein-Barr virus infection - Homo sapiens (human)
  • TGF-Ncore
  • TGF-beta Signaling Pathway
  • tRNA processing

Biological Process

  • mitotic cell cycle
  • mRNA export from nucleus
  • protein import into nucleus
  • protein export from nucleus
  • viral process

Molecular Function

  • nuclear export signal receptor activity
  • protein binding
  • nuclear localization sequence binding
  • structural constituent of nuclear pore

Cellular Component

  • nucleus
  • nuclear pore
  • nucleoplasm
  • cytosol
  • focal adhesion

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000359428
Coding exons
36
Length
109110
Individuals with no LoFs
125688
Homozygous LoFs
0
Heterozygous LoFs
60
Defined
125748
p
0.000239
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.65310631.12e+30.9450.000059313334
Missense (PolyPhen)139173.870.799461905
Synonymous-0.3084594511.020.00002714584
Loss of Function6.532186.50.2430.000004451042

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000450.00043rare
Latino/Admixed American0.000150.00014rare
Ashkenazi Jewish0.000300.00030rare
East Asian0.000220.00022rare
Finnish0.0000920.000092rare
European (Non-Finnish)0.000240.00024rare
South Asian0.000300.00029rare
Other0.000490.00049rare

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: May serve as a docking site in the receptor-mediated import of substrates across the nuclear pore complex. {ECO:0000303|PubMed:8108440}.;
Disease
DISEASE: Note=A chromosomal aberration involving NUP214 is found in a subset of acute myeloid leukemia (AML); also known as acute non-lymphocytic leukemia. Translocation t(6;9)(p23;q34) with DEK. It results in the formation of a DEK-CAN fusion gene. {ECO:0000269|PubMed:1549122}.; DISEASE: Note=A chromosomal aberration involving NUP214 is found in some cases of acute undifferentiated leukemia (AUL). Translocation t(6;9)(q21;q34.1) with SET. {ECO:0000269|PubMed:1630450}.;

Recessive Scores

pRec
0.216

Intolerance Scores

LoFtool
0.247
RVIS EVS
-2.15
RVIS percentile EVS
1.47

Essentials

Essential (CRISPR)
E
Essential (CRISPR2)
E
Essential (gene trap)
E
Indispensability pred.
E
Indispensability score
1.00

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
Feedback | API | MCP | Annotate VCF | Sitemap | About | Privacy & Terms
For research and educational, non-commercial use only. Not for clinical or diagnostic use. GeneBe does not provide medical advice. Data use for AI modeling is prohibited: if used, the cost is $0.001 per byte of downloaded uncompressed data.