NT5C1B

protein-coding

5'-nucleotidase, cytosolic IB, the group of 5'-nucleotidases

Gene summary

Cytosolic 5-prime nucleotidases, such as NT5C1B, catalyze production of adenosine, which regulates diverse physiologic processes (Sala-Newby and Newby, 2001 [PubMed 11690631]).[supplied by OMIM, Mar 2008]

MANE transcript

NM_033253.4

Inheritance

—

ClinVar variants

U:90B:8

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.67

Max pathogenic AF

—

Genomic locus

chr2:18,562,871-18,589,572

External References & Databases

Ensembl (ENSG00000185013)

Transcript & Mutation Effects

hg38 • Region Span ~26.7 kb

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GenCC 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 NT5C1B variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 104

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_033253.4. 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					2 clinvar	2
missense			90 clinvar	5 clinvar		95
nonsense					1 clinvar	1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	90	5	3	98

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_033253.4	RefSeq	NP_150278.2	9	MANE Select
ENST00000304081.9	Ensembl	ENSP00000305979.4	9	MANE Select
NM_001002006.3	RefSeq	NP_001002006.1	10	Standard
NM_001199086.2	RefSeq	NP_001186015.1	10	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)
Nucleobase catabolism
Metabolism of nucleotides

Biological Process

purine nucleotide catabolic process
dephosphorylation

Molecular Function

nucleotide binding
magnesium ion binding
5'-nucleotidase activity

Cellular Component

nucleus
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000359846
Coding exons: 10
Length: 33789
Individuals with no LoFs: 112663
Homozygous LoFs: 697
Heterozygous LoFs: 12388
Defined: 125748
p: 0.0535

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.240	369	382	0.966	0.0000245	3956
Missense (PolyPhen)		119	125.56	0.94773		1333
Synonymous	1.42	131	153	0.854	0.0000104	1206
Loss of Function	1.63	19	28.4	0.669	0.00000127	331

Population LoF Frequency

Population	CAF	p-value	Status
African	0.025	0.024	notable
Latino/Admixed American	0.17	0.15	notable
Ashkenazi Jewish	0.027	0.021	notable
East Asian	0.067	0.060	notable
Finnish	0.12	0.067	notable
European (Non-Finnish)	0.050	0.042	notable
South Asian	0.014	0.012	notable
Other	0.050	0.042	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Dephosphorylates the 5' and 2'(3')-phosphates of deoxyribonucleotides. Helps to regulate adenosine levels (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.156

Intolerance Scores

LoFtool: 0.0808
RVIS EVS: 0.51
RVIS percentile EVS: 80.3

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.00331