NUBP1

Chr 16

NUBP iron-sulfur cluster assembly factor 1, cytosolic

Also known as: CIAO5, NBP, NBP1, NBP35

NCBI Gene: 4682ENSG00000103274UniProt: P53384OMIM: 600280

NUBP1 encodes a component of the cytosolic iron-sulfur protein assembly machinery that forms a scaffold complex with NUBP2 to assemble and transfer iron-sulfur clusters to target proteins, and also regulates centrosome duplication and cilium formation. Mutations cause autosomal recessive multiple mitochondrial dysfunctions syndrome, a severe early-onset disorder affecting multiple organ systems including the brain, liver, and kidneys. The gene shows very low constraint against loss-of-function variants, consistent with recessive inheritance where heterozygous carriers are typically unaffected.

OMIMResearchSummary from RefSeq, UniProt
DNmechanismLOEUF 1.61
Clinical Summary— NUBP1
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
20 unique Pathogenic / Likely Pathogenic· 80 VUS of 121 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.61LOEUF
pLI 0.000
Z-score -0.40
OE 1.11 (0.77–1.61)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
-0.94Z-score
OE missense 1.19 (1.07–1.33)
222 obs / 185.8 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE1.11 (0.77–1.61)
0≤0.351.4
Missense OE1.19 (1.07–1.33)
0≤0.61.4
Synonymous OE1.15
0≤1.21.6
LoF obs/exp: 19 / 17.2Missense obs/exp: 222 / 185.8Syn Z: -1.03
DN
0.6550th %ile
GOF
0.6248th %ile
LOF
0.3453th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

121 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic20
VUS80
Likely Benign5
20
Pathogenic
80
VUS
5
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
20
0
20
Likely Pathogenic
0
0
0
0
0
VUS
1
67
12
0
80
Likely Benign
0
2
1
2
5
Benign
0
0
0
0
0
Total169332105

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

NUBP1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Unraveling the mechanism of [4Fe-4S] cluster assembly on the N-terminal cluster binding site of NUBP1.
Bargagna B et al.·Protein Sci
2023Functional
GLRX3 Acts as a [2Fe-2S] Cluster Chaperone in the Cytosolic Iron-Sulfur Assembly Machinery Transferring [2Fe-2S] Clusters to NUBP1.
Camponeschi F et al.·J Am Chem Soc
2020
Identification of cross-diagnostic biomarkers in ankylosing spondylitis and sarcopenia by bioinformatics and machine learning.
Ka Y et al.·Medicine (Baltimore)
2025
Structure of the HIV-1 reverse transcriptase Q151M mutant: insights into the inhibitor resistance of HIV-1 reverse transcriptase and the structure of the nucleotide-binding pocket of Hepatitis B virus polymerase.
Nakamura A et al.·Acta Crystallogr F Struct Biol Commun
2015
Direct Binding of the Corrector VX-809 to Human CFTR NBD1: Evidence of an Allosteric Coupling between the Binding Site and the NBD1:CL4 Interface.
Hudson RP et al.·Mol Pharmacol
2017
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients