NOB1

NIN1 (RPN12) binding protein 1 homolog, the group of Endoribonucleases|Ribosomal biogenesis factors

Basic information

Region (hg38): 16:69741871-69754926

Previous symbols: [ "PSMD8BP1" ]

Links

ENSG00000141101 ∙ NCBI:28987 ∙ OMIM:613586 ∙ HGNC:29540 ∙ Uniprot:Q9ULX3 ∙ 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 NOB1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NOB1 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	2
missense			29	1		30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	2	1

Variants in NOB1

This is a list of pathogenic ClinVar variants found in the NOB1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-69742430-G-A		not specified	Uncertain significance (Dec 19, 2022)
16-69742476-G-T		not specified	Uncertain significance (Mar 21, 2023)
16-69742484-C-T		not specified	Uncertain significance (Sep 17, 2021)
16-69742485-G-T		not specified	Uncertain significance (Dec 06, 2022)
16-69742546-T-G		not specified	Uncertain significance (May 15, 2024)
16-69742547-C-T		not specified	Uncertain significance (May 02, 2024)
16-69742600-T-A		not specified	Uncertain significance (May 11, 2022)
16-69744875-G-A		not specified	Uncertain significance (Nov 27, 2023)
16-69744907-C-G		not specified	Uncertain significance (Oct 29, 2021)
16-69744932-C-T		not specified	Uncertain significance (Oct 03, 2022)
16-69744986-A-G		not specified	Uncertain significance (Nov 18, 2022)
16-69748233-T-C		not specified	Uncertain significance (Apr 25, 2023)
16-69748252-C-A		not specified	Uncertain significance (Aug 30, 2022)
16-69748269-C-T		not specified	Uncertain significance (Jun 07, 2022)
16-69748274-C-T		not specified	Uncertain significance (Dec 15, 2023)
16-69748287-C-T		not specified	Uncertain significance (Mar 07, 2024)
16-69748926-C-T		not specified	Uncertain significance (Apr 04, 2024)
16-69748929-A-G		not specified	Uncertain significance (Dec 17, 2023)
16-69748947-C-G		not specified	Uncertain significance (Feb 23, 2023)
16-69748950-C-T		not specified	Uncertain significance (Jun 12, 2023)
16-69748962-C-T		not specified	Likely benign (Jul 11, 2023)
16-69749030-C-T		not specified	Uncertain significance (Aug 20, 2023)
16-69749031-C-T		not specified	Uncertain significance (Feb 09, 2023)
16-69749044-G-C		not specified	Uncertain significance (Aug 22, 2023)
16-69749116-A-C		not specified	Uncertain significance (Apr 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NOB1	protein_coding	protein_coding	ENST00000268802	9	13074

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.13e-9	0.324	125697	0	51	125748	0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.607	289	261	1.11	0.0000159	2671
Missense in Polyphen		98	93.922	1.0434		931
Synonymous	-2.27	142	111	1.27	0.00000761	820
Loss of Function	0.836	16	20.0	0.798	0.00000102	224

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000265	0.000265
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000435	0.000435
Finnish	0.00	0.00
European (Non-Finnish)	0.000222	0.000220
Middle Eastern	0.000435	0.000435
South Asian	0.000233	0.000229
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in mRNA degradation.
• Pathway: Ribosome biogenesis in eukaryotes - Homo sapiens (human) (Consensus)

Intolerance Scores

• loftool: 0.721
• rvis_EVS: -0.15
• rvis_percentile_EVS: 42.23

Haploinsufficiency Scores

• pHI: 0.123
• hipred: N
• hipred_score: 0.318
• ghis: 0.525

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.478

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nob1

Gene ontology

• Biological process: cleavage involved in rRNA processing;rRNA processing;visual perception;maturation of SSU-rRNA;RNA phosphodiester bond hydrolysis, endonucleolytic
• Cellular component: nucleoplasm;cytosol;preribosome, small subunit precursor
• Molecular function: endoribonuclease activity;metal ion binding