NUB1

negative regulator of ubiquitin like proteins 1

Basic information

Region (hg38): 7:151341772-151378449

Links

ENSG00000013374 ∙ NCBI:51667 ∙ OMIM:607981 ∙ HGNC:17623 ∙ Uniprot:Q9Y5A7 ∙ 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 NUB1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUB1 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				1		1
missense			7		1	8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	7	1	1

Variants in NUB1

This is a list of pathogenic ClinVar variants found in the NUB1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
7-151345361-G-T			Benign (Dec 31, 2019)
7-151349155-C-A		not specified	Uncertain significance (Nov 09, 2023)
7-151349195-G-A			Likely benign (Nov 01, 2022)
7-151355774-C-T		not specified	Uncertain significance (Jan 23, 2024)
7-151355861-A-G		not specified	Uncertain significance (May 29, 2024)
7-151355894-T-C		not specified	Uncertain significance (Nov 13, 2024)
7-151355956-C-T			Likely benign (Sep 01, 2022)
7-151360159-G-A		not specified	Uncertain significance (Aug 22, 2023)
7-151367922-A-C		not specified	Uncertain significance (Nov 21, 2024)
7-151374097-G-C		not specified	Uncertain significance (Dec 10, 2024)
7-151375918-G-A		not specified	Uncertain significance (Nov 11, 2024)
7-151376637-G-A		not specified	Uncertain significance (Oct 03, 2022)
7-151376697-G-T		not specified	Uncertain significance (Feb 03, 2022)
7-151376710-C-T		not specified	Uncertain significance (Aug 16, 2022)
7-151376796-C-T		not specified	Uncertain significance (Aug 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NUB1	protein_coding	protein_coding	ENST00000568733	15	36751

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000390	1.00	124611	0	35	124646	0.000140

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.36	263	333	0.790	0.0000186	4139
Missense in Polyphen		77	112.88	0.68217		1370
Synonymous	0.619	127	136	0.933	0.00000871	1173
Loss of Function	3.44	12	33.5	0.358	0.00000166	455

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000417	0.000410
Ashkenazi Jewish	0.00	0.00
East Asian	0.000278	0.000278
Finnish	0.00	0.00
European (Non-Finnish)	0.000143	0.000142
Middle Eastern	0.000278	0.000278
South Asian	0.000134	0.000131
Other	0.000165	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Specific down-regulator of the NEDD8 conjugation system. Recruits NEDD8, UBD, and their conjugates to the proteasome for degradation. Isoform 1 promotes the degradation of NEDD8 more efficiently than isoform 2. {ECO:0000269|PubMed:16707496}.
• Pathway: Post-translational protein modification;Metabolism of proteins;Neddylation (Consensus)

Recessive Scores

• pRec: 0.118

Intolerance Scores

• rvis_EVS: -0.33
• rvis_percentile_EVS: 30.7

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.567
• ghis: 0.569

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.732

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Nub1

Gene ontology

• Biological process: ubiquitin-dependent protein catabolic process;protein ubiquitination;positive regulation of proteasomal ubiquitin-dependent protein catabolic process;response to interferon-gamma;response to tumor necrosis factor;post-translational protein modification
• Cellular component: nucleus;cytosol
• Molecular function: protein binding