NT5C3B

5'-nucleotidase, cytosolic IIIB

Basic information

Region (hg38): 17:41825057-41836260

Previous symbols: [ "NT5C3L" ]

Links

ENSG00000141698 ∙ NCBI:115024 ∙ OMIM:620041 ∙ HGNC:28300 ∙ Uniprot:Q969T7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NT5C3B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NT5C3B gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			9	1		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	1	0

Variants in NT5C3B

This is a list of pathogenic ClinVar variants found in the NT5C3B region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
17-41828792-C-T		not specified	Uncertain significance (Mar 20, 2024)
17-41828891-A-G		not specified	Uncertain significance (Jun 30, 2022)
17-41828899-A-G		not specified	Uncertain significance (Apr 13, 2022)
17-41828934-G-T		not specified	Uncertain significance (Nov 24, 2024)
17-41830813-T-C		not specified	Likely benign (Jun 24, 2022)
17-41832401-A-G		not specified	Uncertain significance (Dec 22, 2023)
17-41832446-A-G		not specified	Uncertain significance (Nov 21, 2022)
17-41832458-T-C		not specified	Uncertain significance (Dec 22, 2023)
17-41835081-A-G		not specified	Uncertain significance (Jan 24, 2024)
17-41835102-T-A		not specified	Uncertain significance (Dec 28, 2022)
17-41835206-A-C		not specified	Uncertain significance (Apr 09, 2024)
17-41835272-C-T		not specified	Uncertain significance (Dec 06, 2023)
17-41835888-G-C		not specified	Uncertain significance (Jan 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NT5C3B	protein_coding	protein_coding	ENST00000435506	9	11189

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.66e-10	0.0972	125668	0	80	125748	0.000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.432	158	174	0.908	0.00000915	1991
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000753	0.000752
Ashkenazi Jewish	0.00149	0.00149
East Asian	0.000382	0.000381
Finnish	0.00	0.00
European (Non-Finnish)	0.000190	0.000185
Middle Eastern	0.000382	0.000381
South Asian	0.000588	0.000588
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• 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}.
• Pathway: 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;Deadenylation-dependent mRNA decay (Consensus)

Recessive Scores

• pRec: 0.156

Intolerance Scores

• rvis_EVS: 0.42
• rvis_percentile_EVS: 76.96

Haploinsufficiency Scores

• pHI: 0.116
• hipred: N
• hipred_score: 0.251
• ghis: 0.480

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Nt5c3b

Gene ontology

• Biological process: nucleotide metabolic process;dephosphorylation;exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay
• Cellular component: cytoplasm;cytosol
• Molecular function: nucleotide binding;magnesium ion binding;protein binding;5'-nucleotidase activity