NTPCR

nucleoside-triphosphatase, cancer-related

Basic information

Region (hg38): 1:232950604-232983882

Previous symbols: [ "C1orf57" ]

Links

ENSG00000135778 ∙ NCBI:84284 ∙ ∙ HGNC:28204 ∙ Uniprot:Q9BSD7 ∙ 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 NTPCR gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the NTPCR 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			20	1		21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	1	0

Variants in NTPCR

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

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

Position	Type	Phenotype	Significance	ClinVar
1-232950717-C-T		not specified	Uncertain significance (Jan 26, 2022)
1-232950718-G-C		not specified	Uncertain significance (Mar 01, 2024)
1-232950723-G-C		not specified	Uncertain significance (Apr 29, 2024)
1-232950738-C-T		not specified	Uncertain significance (May 03, 2023)
1-232955580-C-T		not specified	Uncertain significance (Feb 05, 2024)
1-232955679-G-A		not specified	Uncertain significance (Aug 11, 2022)
1-232955691-G-A		not specified	Uncertain significance (Jun 24, 2022)
1-232956360-C-T		not specified	Uncertain significance (Dec 21, 2023)
1-232956419-G-T		not specified	Uncertain significance (Jan 31, 2024)
1-232956423-G-A		not specified	Uncertain significance (Aug 16, 2021)
1-232956432-G-A		not specified	Uncertain significance (Nov 07, 2022)
1-232969945-G-A		not specified	Likely benign (Aug 03, 2022)
1-232969958-T-C		not specified	Uncertain significance (Oct 26, 2021)
1-232969999-G-A		not specified	Uncertain significance (Jan 29, 2024)
1-232970002-C-T		not specified	Uncertain significance (Jul 14, 2021)
1-232970009-C-T		not specified	Uncertain significance (Dec 05, 2022)
1-232970018-C-T		not specified	Uncertain significance (Mar 06, 2023)
1-232970023-G-C		not specified	Uncertain significance (Dec 13, 2023)
1-232970074-C-A		not specified	Uncertain significance (May 04, 2022)
1-232978169-A-G		not specified	Uncertain significance (Oct 27, 2022)
1-232978171-G-C		not specified	Uncertain significance (Oct 10, 2023)
1-232978206-C-T		not specified	Uncertain significance (Jan 05, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
NTPCR	protein_coding	protein_coding	ENST00000366628	5	33278

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00251	0.796	125719	0	29	125748	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.300	103	112	0.920	0.00000670	1210
Missense in Polyphen		32	40.814	0.78404		477
Synonymous	0.224	45	46.9	0.958	0.00000309	395
Loss of Function	1.04	5	8.20	0.610	4.31e-7	99

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000114	0.000114
Middle Eastern	0.0000544	0.0000544
South Asian	0.000369	0.000359
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has nucleotide phosphatase activity towards ATP, GTP, CTP, TTP and UTP. Hydrolyzes nucleoside diphosphates with lower efficiency. {ECO:0000269|PubMed:17291528}.
• Pathway: Purine metabolism - Homo sapiens (human);Thiamine metabolism - Homo sapiens (human);Thiamine Metabolism;UTP and CTP dephosphorylation I;pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis;superpathway of pyrimidine deoxyribonucleotides <i>de novo</i> biosynthesis;pyrimidine deoxyribonucleotides biosynthesis from CTP (Consensus)

Recessive Scores

• pRec: 0.118

Intolerance Scores

• rvis_EVS: 0.42
• rvis_percentile_EVS: 76.81

Haploinsufficiency Scores

• pHI: 0.0984
• hipred: N
• hipred_score: 0.216
• ghis: 0.474

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ntpcr

Gene ontology

• Biological process: dephosphorylation
• Cellular component: membrane
• Molecular function: RNA binding;ATP binding;nucleoside-triphosphatase activity;nucleotide phosphatase activity, acting on free nucleotides