ENTPD1

ectonucleoside triphosphate diphosphohydrolase 1, the group of CD molecules|Ectonucleoside triphosphate diphosphohydrolase family

Basic information

Region (hg38): 10:95711778-95877266

Previous symbols: [ "CD39" ]

Links

ENSG00000138185 ∙ NCBI:953 ∙ OMIM:601752 ∙ HGNC:3363 ∙ Uniprot:P49961 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• 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: CGD

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 ClinVar and linked to the ENTPD1 gene.

• Hereditary spastic paraplegia 64 (116 variants)
• not provided (42 variants)
• Hereditary spastic paraplegia (21 variants)
• Inborn genetic diseases (21 variants)
• Microcephaly;Polymicrogyria;Global developmental delay (1 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			4	30	2	36
missense			66		1	67
nonsense	1		2			3
start loss						0
frameshift	1					1
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region		1	3	6		10
non coding			5	17	21	43
Total	2	0	78	47	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 (Apr 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 (Feb 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		Microcephaly;Polymicrogyria;Global developmental delay • 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: gnomAD

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: dbNSFP

• 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