NT5E
Basic information
Region (hg38): 6:85449584-85495791
Previous symbols: [ "NT5" ]
Links
Phenotypes
GenCC
Source:
- 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:
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
- Inborn_genetic_diseases (74 variants)
- not_provided (16 variants)
- NT5E-related_disorder (15 variants)
- Hereditary_arterial_and_articular_multiple_calcification_syndrome (5 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. These statistics are base on transcript: NM_000002526.4. Only rare variants are included in the table.
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.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 11 | 16 | ||||
missense | 75 | 83 | ||||
nonsense | 4 | |||||
start loss | 0 | |||||
frameshift | 1 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 2 | 2 | 77 | 16 | 7 |
Highest pathogenic variant AF is 0.0000991382
GnomAD
Source:
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:
- 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