NT5M

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

Basic information

Region (hg38): 17:17303335-17347663

Links

ENSG00000205309 ∙ NCBI:56953 ∙ OMIM:605292 ∙ HGNC:15769 ∙ Uniprot:Q9NPB1 ∙ 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 NT5M gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NT5M 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			27	1		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	1	0

Variants in NT5M

This is a list of pathogenic ClinVar variants found in the NT5M region.

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

Position	Type	Phenotype	Significance	ClinVar
17-17303555-T-G		not specified	Uncertain significance (Mar 07, 2025)
17-17303558-G-T		not specified	Uncertain significance (Sep 05, 2024)
17-17303561-T-C		not specified	Uncertain significance (Jan 15, 2025)
17-17303626-G-A		not specified	Uncertain significance (Nov 18, 2023)
17-17303651-G-T		not specified	Uncertain significance (Feb 23, 2025)
17-17303653-G-A		not specified	Uncertain significance (Jan 07, 2022)
17-17303674-A-G		not specified	Uncertain significance (Jun 16, 2023)
17-17303676-G-A		not specified	Uncertain significance (Dec 11, 2024)
17-17303723-G-A		not specified	Uncertain significance (Nov 07, 2024)
17-17303737-G-A		not specified	Uncertain significance (Aug 20, 2024)
17-17303743-C-G		not specified	Uncertain significance (Oct 22, 2021)
17-17303779-G-T		not specified	Uncertain significance (Jan 26, 2023)
17-17303791-T-C		not specified	Uncertain significance (Mar 09, 2025)
17-17303803-C-T		not specified	Uncertain significance (Aug 30, 2022)
17-17306573-A-G		not specified	Uncertain significance (Dec 07, 2024)
17-17306609-G-A		not specified	Uncertain significance (Jun 26, 2024)
17-17306634-G-A		not specified	Likely benign (Oct 05, 2022)
17-17323223-T-G		not specified	Uncertain significance (Dec 28, 2023)
17-17344843-T-A		not specified	Uncertain significance (Apr 17, 2023)
17-17344893-C-T		not specified	Uncertain significance (Sep 25, 2023)
17-17344902-A-C		not specified	Uncertain significance (Jul 02, 2024)
17-17346810-G-A		not specified	Uncertain significance (Nov 10, 2022)
17-17346827-G-C		not specified	Uncertain significance (Jul 14, 2021)
17-17346846-G-A		not specified	Uncertain significance (Mar 08, 2025)
17-17346877-C-A		not specified	Uncertain significance (Jun 22, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NT5M	protein_coding	protein_coding	ENST00000389022	5	44329

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.01e-8	0.0507	125723	0	25	125748	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.178	115	120	0.954	0.00000657	1459
Missense in Polyphen		27	35.751	0.75522		423
Synonymous	-0.673	59	52.8	1.12	0.00000315	470
Loss of Function	-0.692	11	8.79	1.25	3.80e-7	105

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000126	0.000123
Middle Eastern	0.0000544	0.0000544
South Asian	0.000254	0.000229
Other	0.000331	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Dephosphorylates specifically the 5' and 2'(3')- phosphates of uracil and thymine deoxyribonucleotides, and so protects mitochondrial DNA replication from excess dTTP. Has only marginal activity towards dIMP and dGMP. {ECO:0000269|PubMed:10899995}.
• Pathway: Pyrimidine metabolism - Homo sapiens (human);Nicotinate and nicotinamide metabolism - Homo sapiens (human);Purine metabolism - Homo sapiens (human);Pyrimidine metabolism;Pyrimidine catabolism;Nucleobase catabolism;Metabolism of nucleotides;Purine metabolism;Metabolism;Nicotinate Nicotinamide metabolism;Pyrimidine metabolism;Purine nucleotides nucleosides metabolism;Pyrimidine nucleotides nucleosides metabolism (Consensus)

Intolerance Scores

• loftool: 0.671
• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.76

Haploinsufficiency Scores

• pHI: 0.136
• hipred: N
• hipred_score: 0.170
• ghis: 0.508

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0408

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nt5m

Gene ontology

• Biological process: DNA replication;pyrimidine deoxyribonucleotide catabolic process;dephosphorylation;dUMP catabolic process;pyrimidine nucleoside catabolic process
• Cellular component: mitochondrion;mitochondrial matrix
• Molecular function: nucleotide binding;nucleotidase activity;5'-nucleotidase activity;metal ion binding