NOP58

Chr 2

NOP58 ribonucleoprotein

Also known as: HSPC120, NOP5, NOP5/NOP58

NCBI Gene: 51602ENSG00000055044UniProt: Q9Y2X3

The protein encoded by this gene is a core component of box C/D small nucleolar ribonucleoproteins. Some box C/D small nucleolar RNAs (snoRNAs), such as U3, U8, and U14, are dependent upon the encoded protein for their synthesis. This protein is SUMOylated, which is necessary for high affinity binding to snoRNAs. [provided by RefSeq, Nov 2015]

90
ClinVar variants
31
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— NOP58
⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.33) despite low pLI — interpret in context.
📋
ClinVar Variants
31 Pathogenic / Likely Pathogenic· 59 VUS of 90 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.55LOEUF
pLI 0.004
Z-score 3.46
OE 0.33 (0.20–0.55)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
1.55Z-score
OE missense 0.74 (0.66–0.83)
202 obs / 274.1 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.33 (0.20–0.55)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.74 (0.66–0.83)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.04
0≤1.21.6
LoF obs/exp: 10 / 30.6Missense obs/exp: 202 / 274.1Syn Z: -0.33

ClinVar Variant Classifications

90 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic30
Likely Pathogenic1
VUS59
30
Pathogenic
1
Likely Pathogenic
59
VUS

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
30
0
30
Likely Pathogenic
0
0
1
0
1
VUS
0
55
4
0
59
Likely Benign
0
0
0
0
0
Benign
0
0
0
0
0
Total05535090

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

View in ClinVar →

Protein Context — Lollipop Plot

NOP58 · protein map & ClinVar variants

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

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
N6-methyladenosine-modified oncofetal lncRNA MIR4435-2HG contributed to stemness features of hepatocellular carcinoma cells by regulating rRNA 2'-O methylation.
Zhu Y et al.·Cell Mol Biol Lett
2023
Pan-cancer landscape analysis of NOP58 and its oncogenic driving role in lung adenocarcinoma.
Qian S et al.·Sci Rep
2024
Overexpression of NOP58 as a Prognostic Marker in Hepatocellular Carcinoma: A TCGA Data-Based Analysis.
Wang J et al.·Adv Ther
2021
A homozygous synonymous NOP58 variant causes a neurodevelopmental disorder by impairing maturation of pre-ribosomal RNAs.
Bonde LD et al.·HGG Adv
2026
Hepatitis B virus X protein (HBx)-mediated immune modulation and prognostic model development in hepatocellular carcinoma.
Zhong J et al.·PLoS One
2025Functional
Development of a relapse-related RiskScore model to predict the drug sensitivity and prognosis for patients with ovarian cancer.
Jin Z et al.·PeerJ
2025Cohort
Unraveling malignant phenotype of peritumoral tissue: transcriptomic insights into early-stage breast cancer.
Morla-Barcelo PM et al.·Breast Cancer Res
2024
Analysis of the rRNA methylation complex components in pediatric B-cell precursor acute lymphoblastic leukemia: A pilot study.
Ussowicz M et al.·Adv Clin Exp Med
2020
Splice variants denote differences between a cancer stem cell side population of EWSR1‑ERG‑based Ewing sarcoma cells, its main population and EWSR1‑FLI‑based cells.
Korsching E et al.·Int J Mol Med
2022
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools