NTPCR

Chr 1

nucleoside-triphosphatase, cancer-related

Also known as: C1orf57, HCR-NTPase, THEP1

NCBI Gene: 84284 ENSG00000135778 UniProt: Q9BSD7

The encoded protein is a non-specific nucleoside triphosphatase that hydrolyzes ATP, GTP, CTP, TTP and UTP, with lower efficiency toward nucleoside diphosphates. This gene shows low constraint against loss-of-function variants (pLI 0.003, LOEUF 1.28), but no established Mendelian disease associations have been reported in pediatric populations. Overexpression has been observed in tumor tissues, though this appears unrelated to its enzymatic activity.

ResearchSummary from RefSeq, UniProt

The protein encoded by this gene is a non-specific nucleoside triphosphatase that is slow-acting in vitro. This gene is overexpressed in many tumor tissues, and while it is not essential for the cell, overexpression is cytotoxic. However, the cytotoxicity is not related to its triphosphatase activity. [provided by RefSeq, Jul 2016]

ResearchGenerating clinical summary…

DNmechanismLOEUF 1.28

Clinical Summary— NTPCR

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.28LOEUF

pLI 0.003

Z-score 1.04

OE 0.61 (0.32–1.28)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.30Z-score

OE missense 0.92 (0.78–1.08)

103 obs / 111.9 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.61 (0.32–1.28)

0≤0.351.4

Missense OE?0.92 (0.78–1.08)

0≤0.61.4

Synonymous OE?0.96

0≤1.21.6

LoF obs/exp: 5 / 8.2Missense obs/exp: 103 / 111.9Syn Z: 0.22

This gene — mechanism propensity

0.78top 25%

GOF

0.4481th %ile

LOF

0.2968th %ile

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.