NT5C3B

Chr 17

5'-nucleotidase, cytosolic IIIB

Also known as: CNIIIL, NT5C3L, cN-IIIB

NCBI Gene: 115024ENSG00000141698UniProt: Q969T7

Predicted to enable 5'-nucleotidase activity. Predicted to be involved in nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay. Predicted to be located in cytosol. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Jul 2025]

0
Active trials
6
Pathogenic / LP
36
ClinVar variants
5
Pubs (1 yr)
0.4
Missense Z
1.46
LOEUF
Clinical Summary— NT5C3B
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
6 Pathogenic / Likely Pathogenic· 29 VUS of 36 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
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.
1.46LOEUF
pLI 0.000
Z-score 0.19
OE 0.95 (0.63–1.46)
Tolerant

Highly tolerant — LoF variants common in population

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.
0.43Z-score
OE missense 0.91 (0.80–1.04)
158 obs / 174.0 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.0.95 (0.63–1.46)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.91 (0.80–1.04)
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.0.92
0≤1.21.6
LoF obs/exp: 15 / 15.8Missense obs/exp: 158 / 174.0Syn Z: 0.53

ClinVar Variant Classifications

36 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic6
VUS29
Likely Benign1
6
Pathogenic
29
VUS
1
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
6
0
6
Likely Pathogenic
0
0
0
0
0
VUS
0
28
1
0
29
Likely Benign
0
1
0
0
1
Benign
0
0
0
0
0
Total0297036

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

View in ClinVar →

Protein Context — Lollipop Plot

NT5C3B · 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 Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC

No open access results found

Top 5 resultsSearch Europe PMC ↗
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Comparative Genomic Hybridization and Transcriptome Sequencing Reveal Genes with Gain in Acute Lymphoblastic Leukemia: JUP Expression Emerges as a Survival-Related Gene
Zapata-García JA et al.·Diagnostics (Basel)
2022
Investigating the role of cathepsins in breast cancer progression: a Mendelian randomization study
Zhou S et al.·Front Oncol
2025
Genome-wide DNA methylation pattern in whole blood of patients with coal-burning arsenic poisoning.
Wei S et al.·Ecotoxicol Environ Saf
2022Cohort
Bioinformatics analysis identifies NT5M modulates immune evasion through PD-L1 via CXCL8 in pancreatic adenocarcinoma
Zhai C et al.·Sci Rep
2025
Dynamic shifts in trophoblast nucleos(t)ide metabolism, transport, and adenosine signaling during gestation and preterm birth
Ali M et al.·Sci Rep
2025
Genome-wide association study comparison analysis based on Hanwoo full-sib family
Kim JY et al.·Anim Biosci
2024
Gliocidin is a nicotinamide-mimetic prodrug that targets glioblastoma
Chen YJ et al.·Nature
2024
Integrative multi-omics analyses identify key genes and elucidate bidirectional regulatory mechanisms in thyroid dysfunction
Hu Y et al.·PLoS One
2026Functional
Top 8 full-text resultsSearch PubTator3 ↗

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