NEDD8

NEDD8 ubiquitin like modifier

Basic information

Region (hg38): 14:24216856-24232367

Links

ENSG00000129559

∙ NCBI:4738 ∙ OMIM:603171 ∙ HGNC:7732 ∙ Uniprot:Q15843 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NEDD8 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NEDD8 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	0	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NEDD8	protein_coding	protein_coding	ENST00000250495	4	15603

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.849	0.148	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.03	6	43.8	0.137	0.00000229	517
Missense in Polyphen		1	13.768	0.072635		178
Synonymous	1.01	10	15.0	0.667	7.29e-7	155
Loss of Function	2.31	0	6.22	0.00	3.47e-7	69

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Ubiquitin-like protein which plays an important role in cell cycle control and embryogenesis. Covalent attachment to its substrates requires prior activation by the E1 complex UBE1C- APPBP1 and linkage to the E2 enzyme UBE2M. Attachment of NEDD8 to cullins activates their associated E3 ubiquitin ligase activity, and thus promotes polyubiquitination and proteasomal degradation of cyclins and other regulatory proteins. {ECO:0000269|PubMed:10318914, ECO:0000269|PubMed:10597293, ECO:0000269|PubMed:11953428}.;
Pathway: regulation of p27 phosphorylation during cell cycle progression;EGF-EGFR Signaling Pathway;Signal Transduction;Post-translational protein modification;Metabolism of proteins;Transport of small molecules;UCH proteinases;Neddylation;Deubiquitination;Iron uptake and transport;Signaling by TGF-beta Receptor Complex;Signaling by TGF-beta family members;TGF-beta receptor signaling activates SMADs;Validated nuclear estrogen receptor alpha network;Validated nuclear estrogen receptor beta network;p53 pathway (Consensus)

Recessive Scores

pRec: 0.171

Intolerance Scores

loftool
rvis_EVS: 0.1
rvis_percentile_EVS: 60.96

Haploinsufficiency Scores

pHI: 0.557
hipred: Y
hipred_score: 0.740
ghis: 0.543

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.997

Mouse Genome Informatics

Gene name: Nedd8
Phenotype

Gene ontology

Biological process: regulation of transcription by RNA polymerase II;cellular protein modification process;proteolysis;ubiquitin-dependent protein catabolic process;cellular iron ion homeostasis;protein localization;anatomical structure morphogenesis;response to organic cyclic compound;protein ubiquitination;protein deubiquitination;modification-dependent protein catabolic process;regulation of proteolysis;post-translational protein modification;protein neddylation
Cellular component: nucleus;nucleoplasm;cytoplasm;cytosol;extracellular exosome
Molecular function: protein binding;protein tag;ubiquitin protein ligase binding