NUBP1

NUBP iron-sulfur cluster assembly factor 1, cytosolic, the group of Cytosolic iron-sulfur assembly components

Basic information

Region (hg38): 16:10743786-10769351

Previous symbols: [ "NBP1" ]

Links

ENSG00000103274 ∙ NCBI:4682 ∙ OMIM:600280 ∙ HGNC:8041 ∙ Uniprot:P53384 ∙ 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 NUBP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUBP1 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				2		2
missense			42	2		44
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	42	4	0

Variants in NUBP1

This is a list of pathogenic ClinVar variants found in the NUBP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-10743873-G-T		not specified	Uncertain significance (Jun 29, 2023)
16-10743979-G-C		not specified	Uncertain significance (Mar 01, 2024)
16-10743993-A-G		not specified	Uncertain significance (Sep 30, 2024)
16-10743997-G-T		not specified	Uncertain significance (Mar 30, 2024)
16-10744021-A-G		not specified	Uncertain significance (May 28, 2023)
16-10744035-G-C		not specified	Uncertain significance (Dec 27, 2023)
16-10744048-G-C		not specified	Uncertain significance (May 23, 2023)
16-10744050-G-T		not specified	Uncertain significance (Aug 21, 2024)
16-10744053-A-G		not specified	Likely benign (Aug 27, 2024)
16-10747172-A-C		not specified	Uncertain significance (Dec 27, 2023)
16-10747182-A-G		not specified	Uncertain significance (Aug 21, 2023)
16-10747231-C-A		not specified	Uncertain significance (Dec 07, 2023)
16-10747248-A-G		not specified	Uncertain significance (Jul 20, 2021)
16-10752625-A-G		not specified	Uncertain significance (Oct 06, 2023)
16-10752638-G-A		not specified	Uncertain significance (Jun 28, 2024)
16-10752647-T-G		not specified	Uncertain significance (Jun 29, 2023)
16-10752649-C-G		not specified	Uncertain significance (Sep 11, 2024)
16-10752654-G-A			Likely benign (Jan 01, 2023)
16-10752662-G-A		not specified	Uncertain significance (Jan 07, 2022)
16-10752671-G-T		not specified	Uncertain significance (Oct 21, 2024)
16-10755731-G-A		not specified	Uncertain significance (Apr 20, 2024)
16-10756765-G-A		not specified	Uncertain significance (Oct 27, 2023)
16-10756775-A-G		not specified	Uncertain significance (Jun 29, 2022)
16-10757911-G-A		not specified	Uncertain significance (Dec 02, 2022)
16-10757923-C-G		not specified	Uncertain significance (Jun 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NUBP1	protein_coding	protein_coding	ENST00000283027	11	25566

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.73e-14	0.0102	125691	0	56	125747	0.000223

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.943	222	186	1.19	0.0000101	2086
Missense in Polyphen		89	71.556	1.2438		764
Synonymous	-1.03	85	73.8	1.15	0.00000466	604
Loss of Function	-0.404	19	17.2	1.11	7.30e-7	212

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000268	0.000268
Ashkenazi Jewish	0.00	0.00
East Asian	0.000262	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000327	0.000325
Middle Eastern	0.000262	0.000217
South Asian	0.000211	0.000196
Other	0.000349	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the cytosolic iron-sulfur (Fe/S) protein assembly (CIA) machinery (PubMed:18573874). Required for maturation of extramitochondrial Fe-S proteins (PubMed:18573874). The NUBP1-NUBP2 heterotetramer forms a Fe-S scaffold complex, mediating the de novo assembly of an Fe-S cluster and its transfer to target apoproteins (PubMed:18573874). Implicated in the regulation of centrosome duplication (By similarity). Negatively regulates cilium formation and structure (By similarity). {ECO:0000250|UniProtKB:Q9R060, ECO:0000269|PubMed:18573874}.

Recessive Scores

• pRec: 0.0825

Intolerance Scores

• loftool: 0.742
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.54

Haploinsufficiency Scores

• pHI: 0.355
• hipred: N
• hipred_score: 0.294
• ghis: 0.518

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.782

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nubp1
• Phenotype: respiratory system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); limbs/digits/tail phenotype; vision/eye phenotype

Gene ontology

• Biological process: regulation of cell growth;cellular iron ion homeostasis;negative regulation of centrosome duplication;iron-sulfur cluster assembly;cell projection organization;centrosome localization;protein localization to cell cortex
• Cellular component: nucleus;centriole;cytosol;plasma membrane;cilium
• Molecular function: nucleotide binding;protein binding;ATP binding;metal ion binding;iron-sulfur cluster binding;4 iron, 4 sulfur cluster binding