NT5C

5', 3'-nucleotidase, cytosolic, the group of 5'-nucleotidases

Basic information

Region (hg38): 17:75130225-75131757

Previous symbols: [ "UMPH2" ]

Links

ENSG00000125458 ∙ NCBI:30833 ∙ OMIM:191720 ∙ HGNC:17144 ∙ Uniprot:Q8TCD5 ∙ 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 NT5C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NT5C 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			24	1		25
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	1	0

Variants in NT5C

This is a list of pathogenic ClinVar variants found in the NT5C region.

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

Position	Type	Phenotype	Significance	ClinVar
17-75130492-T-A		not specified	Uncertain significance (Jun 22, 2021)
17-75130565-T-C		not specified	Uncertain significance (Feb 14, 2023)
17-75130567-G-C		not specified	Uncertain significance (Aug 02, 2021)
17-75130589-G-C		not specified	Uncertain significance (Jul 13, 2022)
17-75130759-C-T		not specified	Likely benign (Feb 17, 2022)
17-75130777-T-C		not specified	Uncertain significance (Jun 11, 2021)
17-75130813-T-C		not specified	Uncertain significance (Jan 04, 2024)
17-75131064-T-C		not specified	Uncertain significance (Oct 25, 2024)
17-75131079-G-C		not specified	Uncertain significance (Jun 19, 2024)
17-75131191-C-A		not specified	Uncertain significance (May 28, 2024)
17-75131200-C-T		not specified	Uncertain significance (Jan 14, 2025)
17-75131206-C-A		not specified	Uncertain significance (Nov 30, 2021)
17-75131564-C-G		not specified	Uncertain significance (Oct 25, 2024)
17-75131569-G-T		not specified	Uncertain significance (Jun 18, 2021)
17-75131577-A-G		not specified	Uncertain significance (Jun 01, 2023)
17-75131581-C-T		not specified	Uncertain significance (Jul 27, 2024)
17-75131593-C-T		not specified	Uncertain significance (Nov 18, 2022)
17-75131599-G-A		not specified	Uncertain significance (Nov 21, 2023)
17-75131626-G-A		not specified	Uncertain significance (May 17, 2023)
17-75131634-C-T		not specified	Uncertain significance (Oct 17, 2023)
17-75131638-G-A		not specified	Uncertain significance (Nov 18, 2022)
17-75131646-C-T		not specified	Uncertain significance (Jul 09, 2021)
17-75131677-T-C		not specified	Uncertain significance (Nov 08, 2024)
17-75131686-G-C		not specified	Uncertain significance (Nov 21, 2024)
17-75131689-C-G		not specified	Uncertain significance (May 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NT5C	protein_coding	protein_coding	ENST00000245552	5	1571

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00273	0.811	125711	0	34	125745	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.252	108	101	1.07	0.00000543	1267
Missense in Polyphen		42	42.962	0.97761		611
Synonymous	0.601	38	43.0	0.883	0.00000225	406
Loss of Function	1.08	5	8.37	0.597	4.10e-7	93

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000214	0.000213
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000220	0.000220
Middle Eastern	0.000218	0.000217
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Dephosphorylates the 5' and 2'(3')-phosphates of deoxyribonucleotides, with a preference for dUMP and dTMP, intermediate activity towards dGMP, and low activity towards dCMP and dAMP.
• Pathway: Pyrimidine metabolism - Homo sapiens (human);Nicotinate and nicotinamide metabolism - Homo sapiens (human);Purine metabolism - Homo sapiens (human);Lamivudine Pathway, Pharmacokinetics/Pharmacodynamics;Gemcitabine Pathway, Pharmacodynamics;Gemcitabine Action Pathway;Lamivudine Metabolism Pathway;Gemcitabine Metabolism Pathway;Pyrimidine metabolism;Pyrimidine catabolism;Nucleobase catabolism;Metabolism of nucleotides;Purine metabolism;Vitamin B3 (nicotinate and nicotinamide) metabolism;Metabolism;Nicotinate Nicotinamide metabolism;Pyrimidine metabolism;Purine nucleotides nucleosides metabolism;Pyrimidine nucleotides nucleosides metabolism;Purine catabolism (Consensus)

Intolerance Scores

• loftool: 0.608
• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.95

Haploinsufficiency Scores

• pHI: 0.0821
• hipred: N
• hipred_score: 0.170
• ghis: 0.547

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0317

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nt5c

Gene ontology

• Biological process: purine nucleotide catabolic process;pyrimidine deoxyribonucleotide catabolic process;dephosphorylation;pyrimidine nucleoside catabolic process
• Cellular component: nucleus;cytoplasm;cytosol;extracellular exosome
• Molecular function: nucleotidase activity;5'-nucleotidase activity;pyrimidine nucleotide binding;metal ion binding