NT5C3B
protein-coding5'-nucleotidase, cytosolic IIIB
Gene summary
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]
- NT5C3L
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~11.2 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to NT5C3B variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_052935.5. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 32 | 1 | 33 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 35 | 1 | 0 | 36 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_443167.4 | 9 | MANE Select | |
| Ensembl | ENSP00000389948.2 | 9 | MANE Select | |
| Ensembl | ENSP00000397742.1 | 8 | Standard | |
| Ensembl | ENSP00000392092.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Pyrimidine metabolism - Homo sapiens (human)
- Nicotinate and nicotinamide metabolism - Homo sapiens (human)
- Purine metabolism - Homo sapiens (human)
- Metabolism of RNA
- mRNA decay by 3, to 5, exoribonuclease
Biological Process
- nucleotide metabolic process
- dephosphorylation
- exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay
Molecular Function
- nucleotide binding
- magnesium ion binding
- protein binding
- 5'-nucleotidase activity
Cellular Component
- cytoplasm
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000435506
- Coding exons
- 9
- Length
- 11189
- Individuals with no LoFs
- 125668
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 80
- Defined
- 125748
- p
- 0.000318
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.432 | 158 | 174 | 0.908 | 0.00000915 | 1991 |
| Missense (PolyPhen) | 62 | 69.651 | 0.89015 | 820 | ||
| Synonymous | 0.526 | 62 | 67.5 | 0.919 | 0.00000365 | 550 |
| Loss of Function | 0.192 | 15 | 15.8 | 0.948 | 8.40e-7 | 183 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00049 | 0.00049 | rare |
| Latino/Admixed American | 0.00026 | 0.00026 | rare |
| Ashkenazi Jewish | 0.0015 | 0.0015 | notable |
| East Asian | 0.00038 | 0.00038 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00019 | 0.00018 | rare |
| South Asian | 0.00059 | 0.00059 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Specifically hydrolyzes 7-methylguanosine monophosphate (m(7)GMP) to 7-methylguanosine and inorganic phosphate (PubMed:23223233, PubMed:24603684). The specific activity for m(7)GMP may protect cells against undesired salvage of m(7)GMP and its incorporation into nucleic acids (PubMed:23223233). Also has weak activity for CMP (PubMed:23223233, PubMed:24603684). UMP and purine nucleotides are poor substrates (PubMed:23223233). {ECO:0000269|PubMed:23223233, ECO:0000269|PubMed:24603684}.;
Recessive Scores
- pRec
- 0.156
Intolerance Scores
- RVIS EVS
- 0.42
- RVIS percentile EVS
- 76.96
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |