NUBP2

NUBP iron-sulfur cluster assembly factor 2, cytosolic, the group of Cytosolic iron-sulfur assembly components

Basic information

Region (hg38): 16:1782932-1789186

Links

ENSG00000095906 ∙ NCBI:10101 ∙ OMIM:610779 ∙ HGNC:8042 ∙ Uniprot:Q9Y5Y2 ∙ 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 NUBP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NUBP2 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			26	1	1	28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	2	2

Variants in NUBP2

This is a list of pathogenic ClinVar variants found in the NUBP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-1786557-G-A		not specified	Likely benign (Apr 17, 2024)
16-1786615-C-T		not specified	Uncertain significance (Jun 28, 2022)
16-1786618-C-T		not specified	Uncertain significance (Jun 01, 2023)
16-1786838-G-A		not specified	Uncertain significance (Sep 16, 2021)
16-1786863-T-G		not specified	Uncertain significance (Apr 07, 2023)
16-1786868-C-T		not specified	Uncertain significance (Nov 18, 2023)
16-1786871-G-C		not specified	Uncertain significance (Dec 19, 2022)
16-1786882-C-G		not specified	Uncertain significance (Mar 20, 2023)
16-1786893-C-G		not specified	Uncertain significance (Dec 15, 2023)
16-1786895-G-C		not specified	Uncertain significance (Aug 04, 2023)
16-1786916-C-T		not specified	Uncertain significance (May 31, 2022)
16-1786922-G-A		not specified	Uncertain significance (Aug 26, 2022)
16-1786928-G-A		not specified	Uncertain significance (Sep 01, 2021)
16-1786934-T-C		not specified	Uncertain significance (May 05, 2023)
16-1786955-G-A			Uncertain significance (Nov 01, 2018)
16-1787682-A-G		not specified	Uncertain significance (Dec 06, 2022)
16-1787690-G-C		not specified	Uncertain significance (Dec 13, 2023)
16-1787703-G-A		not specified	Uncertain significance (Dec 13, 2023)
16-1787740-C-T		not specified	Uncertain significance (Dec 03, 2021)
16-1787776-T-C		not specified	Uncertain significance (Oct 25, 2023)
16-1787942-C-T		not specified	Uncertain significance (Jun 09, 2022)
16-1787990-C-T			Benign (Apr 03, 2018)
16-1787999-G-A		not specified	Likely benign (May 20, 2024)
16-1788017-A-G		not specified	Uncertain significance (Apr 26, 2024)
16-1788050-C-T		not specified	Uncertain significance (Apr 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NUBP2	protein_coding	protein_coding	ENST00000262302	7	6291

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000921	0.817	125471	0	21	125492	0.0000837

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0721	182	179	1.02	0.0000120	1717
Missense in Polyphen		73	72.003	1.0138		747
Synonymous	-1.52	105	86.9	1.21	0.00000691	576
Loss of Function	1.14	6	9.86	0.609	4.18e-7	125

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000618	0.0000617
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.0000444	0.0000441
Middle Eastern	0.000164	0.000163
South Asian	0.000393	0.000392
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the cytosolic iron-sulfur (Fe/S) protein assembly (CIA) machinery. Required for maturation of extramitochondrial Fe-S proteins. 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. Negatively regulates cilium formation and structure. {ECO:0000250|UniProtKB:Q9R061, ECO:0000255|HAMAP-Rule:MF_03039}.

Recessive Scores

• pRec: 0.131

Intolerance Scores

• loftool: 0.675
• rvis_EVS: -0.58
• rvis_percentile_EVS: 18.78

Haploinsufficiency Scores

• pHI: 0.0857
• hipred: N
• hipred_score: 0.231
• ghis: 0.552

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.798

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nubp2

Gene ontology

• Biological process: iron-sulfur cluster assembly;cell projection organization
• Cellular component: nucleus;centriole;cytosol;cilium;spindle pole centrosome
• Molecular function: nucleotide binding;protein binding;ATP binding;metal ion binding;iron-sulfur cluster binding;4 iron, 4 sulfur cluster binding