ENTPD1
Basic information
Region (hg38): 10:95711779-95877266
Previous symbols: [ "CD39" ]
Links
Phenotypes
GenCC
Source:
- hereditary spastic paraplegia 64 (Moderate), mode of inheritance: AR
- hereditary spastic paraplegia 64 (Strong), mode of inheritance: AR
- hereditary spastic paraplegia 64 (Limited), mode of inheritance: AR
- hereditary spastic paraplegia 64 (Supportive), mode of inheritance: AR
- hereditary spastic paraplegia 64 (Limited), mode of inheritance: AR
- complex hereditary spastic paraplegia (Definitive), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Spastic paraplegia 64, autosomal recessive | 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 | Neurologic | 24482476 |
ClinVar
This is a list of variants' phenotypes submitted to
- Hereditary spastic paraplegia 64 (3 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ENTPD1 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 | 35 | 41 | ||||
missense | 72 | 73 | ||||
nonsense | 4 | |||||
start loss | 0 | |||||
frameshift | 1 | |||||
inframe indel | 1 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 1 | 3 | 6 | 10 | ||
non coding | 23 | 21 | 49 | |||
Total | 3 | 0 | 84 | 58 | 24 |
Variants in ENTPD1
This is a list of pathogenic ClinVar variants found in the ENTPD1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
10-95711826-T-C | Likely benign (Apr 09, 2021) | |||
10-95711989-G-A | Conflicting classifications of pathogenicity (Aug 01, 2024) | |||
10-95712168-T-C | Benign (Nov 11, 2018) | |||
10-95727661-T-G | Uncertain significance (Jul 05, 2023) | |||
10-95755380-G-A | Hereditary spastic paraplegia 64 | Benign (Nov 29, 2022) | ||
10-95755766-G-A | Hereditary spastic paraplegia 64 | Conflicting classifications of pathogenicity (Jul 01, 2024) | ||
10-95755831-T-C | Benign (Apr 08, 2021) | |||
10-95756154-A-C | Hereditary spastic paraplegia | Uncertain significance (Dec 22, 2016) | ||
10-95756268-T-C | Hereditary spastic paraplegia 64 | Likely benign (Dec 03, 2021) | ||
10-95756521-GT-G | Benign (Apr 16, 2021) | |||
10-95823211-T-C | Likely benign (May 11, 2021) | |||
10-95823221-C-T | Hereditary spastic paraplegia 64 | Likely benign (Jan 08, 2024) | ||
10-95823224-C-T | Hereditary spastic paraplegia 64 | Likely benign (Jul 12, 2023) | ||
10-95823239-T-G | Hereditary spastic paraplegia 64 • Inborn genetic diseases | Uncertain significance (May 24, 2023) | ||
10-95823244-C-T | Hereditary spastic paraplegia 64 • ENTPD1-related disorder | Likely benign (Feb 01, 2023) | ||
10-95823245-G-A | Global developmental delay;Microcephaly;Polymicrogyria • Hereditary spastic paraplegia 64 • Hereditary spastic paraplegia | Uncertain significance (Sep 12, 2022) | ||
10-95823249-A-C | Inborn genetic diseases | Uncertain significance (Aug 08, 2022) | ||
10-95823259-C-T | Hereditary spastic paraplegia 64 | Likely benign (Jan 22, 2024) | ||
10-95823263-A-G | Hereditary spastic paraplegia 64 | Uncertain significance (Sep 19, 2023) | ||
10-95823284-G-T | Inborn genetic diseases | Uncertain significance (Jan 07, 2022) | ||
10-95823298-C-G | Hereditary spastic paraplegia 64 | Uncertain significance (Sep 10, 2021) | ||
10-95823354-A-C | Inborn genetic diseases | Uncertain significance (Mar 20, 2023) | ||
10-95823358-C-T | Hereditary spastic paraplegia 64 | Likely benign (Oct 31, 2022) | ||
10-95823359-G-A | Hereditary spastic paraplegia | Uncertain significance (Jun 01, 2019) | ||
10-95823374-A-G | Hereditary spastic paraplegia 64 | Uncertain significance (May 26, 2020) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
ENTPD1 | protein_coding | protein_coding | ENST00000371207 | 10 | 165488 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.00807 | 0.991 | 125738 | 0 | 10 | 125748 | 0.0000398 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.832 | 226 | 264 | 0.856 | 0.0000130 | 3467 |
Missense in Polyphen | 68 | 98.714 | 0.68886 | 1301 | ||
Synonymous | 1.09 | 89 | 103 | 0.863 | 0.00000573 | 967 |
Loss of Function | 3.02 | 8 | 24.0 | 0.334 | 0.00000104 | 303 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000120 | 0.000120 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000440 | 0.0000439 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.0000327 | 0.0000327 |
Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: In the nervous system, could hydrolyze ATP and other nucleotides to regulate purinergic neurotransmission. Could also be implicated in the prevention of platelet aggregation by hydrolyzing platelet-activating ADP to AMP. Hydrolyzes ATP and ADP equally well. {ECO:0000269|PubMed:8955160}.;
- Disease
- DISEASE: Spastic paraplegia 64, autosomal recessive (SPG64) [MIM:615683]: A form of spastic paraplegia, a neurodegenerative disorder characterized by a slow, gradual, progressive weakness and spasticity of the lower limbs. Rate of progression and the severity of symptoms are quite variable. Initial symptoms may include difficulty with balance, weakness and stiffness in the legs, muscle spasms, and dragging the toes when walking. In some forms of the disorder, bladder symptoms (such as incontinence) may appear, or the weakness and stiffness may spread to other parts of the body. {ECO:0000269|PubMed:24482476}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
- Pathway
- Pyrimidine metabolism - Homo sapiens (human);Purine metabolism - Homo sapiens (human);Epstein-Barr virus infection - Homo sapiens (human);Pyrimidine metabolism;Nucleobase catabolism;Metabolism of nucleotides;UTP and CTP dephosphorylation II;Phosphate bond hydrolysis by NTPDase proteins;Purine metabolism;Metabolism;Pyrimidine metabolism;Purine nucleotides nucleosides metabolism;Pyrimidine nucleotides nucleosides metabolism
(Consensus)
Recessive Scores
- pRec
- 0.239
Intolerance Scores
- loftool
- 0.568
- rvis_EVS
- -0.34
- rvis_percentile_EVS
- 30.56
Haploinsufficiency Scores
- pHI
- 0.174
- hipred
- N
- hipred_score
- 0.334
- ghis
- 0.598
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.189
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Entpd1
- Phenotype
- behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; respiratory 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); hematopoietic system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; immune system phenotype; skeleton phenotype; renal/urinary system phenotype; muscle phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- cell adhesion;blood coagulation;nucleobase-containing small molecule catabolic process
- Cellular component
- plasma membrane;integral component of plasma membrane;membrane;extracellular exosome
- Molecular function
- protein binding;ATP binding;nucleoside-diphosphatase activity;nucleoside-triphosphatase activity;dATP phosphohydrolase activity;dCTP phosphohydrolase activity;dUTP phosphohydrolase activity;dTTP phosphohydrolase activity;GTP phosphohydrolase activity;8-oxo-dGTP phosphohydrolase activity;dGTP phosphohydrolase activity