NT5C1B

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

Basic information

Region (hg38): 2:18562870-18589572

Links

ENSG00000185013 ∙ NCBI:93034 ∙ OMIM:610526 ∙ HGNC:17818 ∙ Uniprot:Q96P26 ∙ 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 NT5C1B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NT5C1B 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					3	3
missense			47	4		51
nonsense					1	1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	47	4	4

Variants in NT5C1B

This is a list of pathogenic ClinVar variants found in the NT5C1B region.

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

Position	Type	Phenotype	Significance	ClinVar
2-18563806-A-G		not specified	Uncertain significance (Feb 26, 2024)
2-18563818-A-G		not specified	Uncertain significance (Oct 02, 2023)
2-18563821-C-A		not specified	Uncertain significance (Apr 17, 2023)
2-18563831-C-T		not specified	Likely benign (Jan 05, 2022)
2-18563860-A-G		not specified	Uncertain significance (Dec 01, 2022)
2-18563897-G-A		not specified	Uncertain significance (Mar 20, 2024)
2-18563975-G-A		not specified	Uncertain significance (Oct 27, 2023)
2-18564038-T-C		not specified	Uncertain significance (Apr 18, 2023)
2-18564053-G-A		not specified	Uncertain significance (Jun 06, 2023)
2-18564104-A-G		not specified	Uncertain significance (Dec 21, 2022)
2-18576241-A-T		not specified	Uncertain significance (Jan 26, 2022)
2-18576242-T-C		not specified	Uncertain significance (Mar 20, 2023)
2-18576309-G-A		not specified	Uncertain significance (Jun 30, 2022)
2-18576819-C-G		not specified	Uncertain significance (Sep 26, 2023)
2-18582970-G-A		not specified	Uncertain significance (Nov 02, 2023)
2-18584098-C-G		not specified	Uncertain significance (Dec 16, 2023)
2-18584132-C-T		not specified	Uncertain significance (Jan 23, 2024)
2-18584165-G-T		not specified	Uncertain significance (May 17, 2023)
2-18584197-A-C		not specified	Uncertain significance (Dec 28, 2023)
2-18584199-C-G		not specified	Uncertain significance (Oct 26, 2022)
2-18584218-G-A		not specified	Uncertain significance (Jan 03, 2024)
2-18584219-A-T		not specified	Uncertain significance (Jan 27, 2022)
2-18584534-T-C		not specified	Uncertain significance (Jun 29, 2023)
2-18584600-C-G		not specified	Uncertain significance (Jun 24, 2022)
2-18584605-T-C		not specified	Uncertain significance (Jun 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NT5C1B	protein_coding	protein_coding	ENST00000359846	10	33789

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.54e-10	0.807	112663	697	12388	125748	0.0535

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.240	369	382	0.966	0.0000245	3956
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.193	0.192
Ashkenazi Jewish	0.0272	0.0212
East Asian	0.0668	0.0601
Finnish	0.119	0.0669
European (Non-Finnish)	0.0503	0.0418
Middle Eastern	0.0668	0.0601
South Asian	0.0141	0.0121
Other	0.0505	0.0424

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Dephosphorylates the 5' and 2'(3')-phosphates of deoxyribonucleotides. Helps to regulate adenosine levels (By similarity). {ECO:0000250}.
• Pathway: Pyrimidine metabolism - Homo sapiens (human);Nicotinate and nicotinamide metabolism - Homo sapiens (human);Purine metabolism - Homo sapiens (human);Nucleobase catabolism;Metabolism of nucleotides;Purine metabolism;adenosine nucleotides degradation;purine nucleotides degradation;Vitamin B3 (nicotinate and nicotinamide) metabolism;Metabolism;Nicotinate Nicotinamide metabolism;Pyrimidine metabolism;Purine nucleotides nucleosides metabolism;Pyrimidine nucleotides nucleosides metabolism;Purine catabolism (Consensus)

Recessive Scores

• pRec: 0.156

Intolerance Scores

• loftool: 0.0808
• rvis_EVS: 0.51
• rvis_percentile_EVS: 80.3

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.132

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00331

Mouse Genome Informatics

• Gene name: Nt5c1b

Gene ontology

• Biological process: purine nucleotide catabolic process;dephosphorylation
• Cellular component: nucleus;cytosol
• Molecular function: nucleotide binding;magnesium ion binding;5'-nucleotidase activity