NT5E

5'-nucleotidase ecto, the group of 5'-nucleotidases|CD molecules

Basic information

Region (hg38): 6:85449583-85495791

Previous symbols: [ "NT5" ]

Links

ENSG00000135318 ∙ NCBI:4907 ∙ OMIM:129190 ∙ HGNC:8021 ∙ Uniprot:P21589 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• hereditary arterial and articular multiple calcification syndrome (Moderate), mode of inheritance: AR
• hereditary arterial and articular multiple calcification syndrome (Strong), mode of inheritance: AR
• hereditary arterial and articular multiple calcification syndrome (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Calcification of joints and arteries	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Cardiovascular; Musculoskeletal	21288095

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the NT5E gene.

• Inborn genetic diseases (25 variants)
• not provided (16 variants)
• Hereditary arterial and articular multiple calcification syndrome (5 variants)
• NT5E-related condition (3 variants)
• NT5E-Related Disorder (2 variants)
• not specified (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NT5E 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				5	4	9
missense			27	3	3	33
nonsense		1				1
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	2	27	8	8

Highest pathogenic variant AF is 0.0000394

Variants in NT5E

This is a list of pathogenic ClinVar variants found in the NT5E region.

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

Position	Type	Phenotype	Significance	ClinVar
6-85450149-C-G		Inborn genetic diseases	Uncertain significance (Jul 20, 2022)
6-85450157-G-C		NT5E-related disorder	Likely benign (Sep 08, 2023)
6-85450158-C-G		Inborn genetic diseases	Uncertain significance (Jul 06, 2021)
6-85450167-G-C		Inborn genetic diseases	Uncertain significance (Oct 20, 2021)
6-85450170-A-G		Inborn genetic diseases	Uncertain significance (Aug 09, 2021)
6-85450174-T-G		Inborn genetic diseases	Uncertain significance (Aug 02, 2021)
6-85450181-C-T			Benign (Jul 13, 2018)
6-85450186-T-G		Inborn genetic diseases	Uncertain significance (Feb 10, 2022)
6-85450215-G-T		NT5E-related disorder	Likely benign (Aug 31, 2023)
6-85450239-A-G		Inborn genetic diseases	Uncertain significance (Jul 11, 2023)
6-85450311-A-G		Inborn genetic diseases	Likely benign (Oct 27, 2022)
6-85450346-G-T		Inborn genetic diseases	Uncertain significance (Feb 22, 2023)
6-85450362-G-T		NT5E-related disorder	not provided (-)
6-85450452-A-G		Inborn genetic diseases	Uncertain significance (Sep 21, 2023)
6-85467062-A-G			Benign (Dec 31, 2019)
6-85467164-G-A			Likely benign (Jul 13, 2018)
6-85467171-G-C		Inborn genetic diseases	Uncertain significance (Apr 04, 2023)
6-85467177-C-G		NT5E-related disorder	Benign/Likely benign (Jul 15, 2020)
6-85467183-T-A		Inborn genetic diseases	Uncertain significance (May 16, 2022)
6-85467248-C-T			Benign (Dec 31, 2019)
6-85471243-A-C		Inborn genetic diseases	Uncertain significance (Apr 24, 2023)
6-85471336-C-A		Hereditary arterial and articular multiple calcification syndrome	Pathogenic (Feb 03, 2011)
6-85471419-T-C		Inborn genetic diseases	Uncertain significance (Dec 07, 2023)
6-85485261-G-C		Inborn genetic diseases	Uncertain significance (Jun 02, 2023)
6-85485306-G-C		Inborn genetic diseases	Uncertain significance (Feb 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NT5E	protein_coding	protein_coding	ENST00000257770	9	45692

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.29e-11	0.243	125651	0	97	125748	0.000386

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.604	291	321	0.905	0.0000166	3733
Missense in Polyphen		88	103.71	0.84852		1154
Synonymous	1.01	112	126	0.886	0.00000683	1135
Loss of Function	0.877	19	23.6	0.805	0.00000117	288

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00120	0.00120
Ashkenazi Jewish	0.000496	0.000496
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000512	0.000484
Middle Eastern	0.00	0.00
South Asian	0.000133	0.000131
Other	0.000506	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Hydrolyzes extracellular nucleotides into membrane permeable nucleosides. Exhibits AMP-, NAD-, and NMN-nucleosidase activities. {ECO:0000269|PubMed:21933152}.
• Disease: DISEASE: Calcification of joints and arteries (CALJA) [MIM:211800]: A condition characterized by adult-onset calcification of the lower extremity arteries, including the iliac, femoral and tibial arteries, and hand and foot capsule joints. Age of onset has been reported as early as the second decade of life, usually involving intense joint pain or calcification in the hands. {ECO:0000269|PubMed:21288095, ECO:0000269|PubMed:24887587}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Pyrimidine metabolism - Homo sapiens (human);Nicotinate and nicotinamide metabolism - Homo sapiens (human);Purine metabolism - Homo sapiens (human);Thiopurine Pathway, Pharmacokinetics/Pharmacodynamics;miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Differentiation Pathway;NAD+ metabolism;Pyrimidine catabolism;Nucleobase catabolism;Metabolism of nucleotides;Purine metabolism;urate biosynthesis/inosine 5,-phosphate degradation;adenosine nucleotides degradation;purine nucleotides degradation;Vitamin B3 (nicotinate and nicotinamide) metabolism;Metabolism;Nicotinate Nicotinamide metabolism;Nicotinate metabolism;Metabolism of water-soluble vitamins and cofactors;Pyrimidine metabolism;Metabolism of vitamins and cofactors;Purine nucleotides nucleosides metabolism;Pyrimidine nucleotides nucleosides metabolism;Purine catabolism;HIF-1-alpha transcription factor network (Consensus)

Recessive Scores

• pRec: 0.463

Intolerance Scores

• loftool: 0.512
• rvis_EVS: 0.04
• rvis_percentile_EVS: 57.41

Haploinsufficiency Scores

• pHI: 0.219
• hipred: N
• hipred_score: 0.390
• ghis: 0.443

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.262

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Nt5e
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); homeostasis/metabolism phenotype; renal/urinary system phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; craniofacial phenotype

Gene ontology

• Biological process: purine nucleotide catabolic process;AMP catabolic process;DNA metabolic process;leukocyte cell-cell adhesion;dephosphorylation;NAD metabolic process;adenosine biosynthetic process;pyrimidine nucleoside catabolic process;negative regulation of inflammatory response
• Cellular component: nucleoplasm;cytosol;plasma membrane;cell surface;membrane;anchored component of membrane;extracellular exosome
• Molecular function: nucleotide binding;5'-nucleotidase activity;metal ion binding