NT5C1A

Chr 1

5'-nucleotidase, cytosolic IA

Also known as: CN-I, CN-IA, CN1, CN1A, CNI

NCBI Gene: 84618ENSG00000116981UniProt: Q9BXI3

Cytosolic nucleotidases, such as NT5C1A, dephosphorylate nucleoside monophosphates (Hunsucker et al., 2001 [PubMed 11133996]).[supplied by OMIM, Mar 2008]

63
ClinVar variants
8
Pathogenic / LP
0.00
pLI score
0
Active trials
Clinical Summary— NT5C1A
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
8 Pathogenic / Likely Pathogenic· 45 VUS of 63 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.
0.96LOEUF
pLI 0.000
Z-score 1.68
OE 0.55 (0.33–0.96)
Tolerant

Typical tolerance to LoF variation

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.
0.87Z-score
OE missense 0.84 (0.75–0.95)
209 obs / 247.3 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.0.55 (0.33–0.96)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.84 (0.75–0.95)
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.1.01
0≤1.21.6
LoF obs/exp: 9 / 16.3Missense obs/exp: 209 / 247.3Syn Z: -0.09

ClinVar Variant Classifications

63 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic6
Likely Pathogenic2
VUS45
Likely Benign2
Benign3
6
Pathogenic
2
Likely Pathogenic
45
VUS
2
Likely Benign
3
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
6
0
6
Likely Pathogenic
0
0
2
0
2
VUS
0
41
4
0
45
Likely Benign
0
1
1
0
2
Benign
0
1
0
2
3
Total04313258

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

View in ClinVar →

Protein Context — Lollipop Plot

NT5C1A · 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
Inclusion Body Myositis.
Greenberg SA·Continuum (Minneap Minn)
2016Review
Autoantibodies against a subunit of mitochondrial respiratory chain complex I in inclusion body myositis.
Notarnicola A et al.·J Autoimmun
2024
Cytosolic 5'-Nucleotidase 1A As a Target of Circulating Autoantibodies in Autoimmune Diseases.
Lloyd TE et al.·Arthritis Care Res (Hoboken)
2016
Clinical utility of anti-cytosolic 5'-nucleotidase 1A antibody in idiopathic inflammatory myopathies.
Ikenaga C et al.·Ann Clin Transl Neurol
2021
Clinical significance of anti-NT5c1A autoantibody in Korean patients with inflammatory myopathies.
Lee SA et al.·PLoS One
2023Cohort
Anti-NT5c1A Autoantibodies as Biomarkers in Inclusion Body Myositis.
Amlani A et al.·Front Immunol
2019
The clinico-serological spectrum of overlap myositis.
Fredi M et al.·Curr Opin Rheumatol
2018Review
Anti-NT5C1A autoantibodies are associated with more severe disease in patients with juvenile myositis.
Yeker RM et al.·Ann Rheum Dis
2018Cohort
Pharmacogenetic characterization of naturally occurring germline NT5C1A variants to chemotherapeutic nucleoside analogs.
Saliba J et al.·Pharmacogenet Genomics
2016
Coexistence of CN1A autoantibodies in GAD65 encephalitis exacerbates neurodegeneration : Novel autoantibodies in GAD65 encephalitis.
Breuer A et al.·J Neuroinflammation
2025
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