NT5C2

Chr 10AR

5'-nucleotidase, cytosolic II

Also known as: GMP, NT5B, PNT5, SPG45, SPG65, cN-II

This gene encodes a hydrolase that serves as an important role in cellular purine metabolism by acting primarily on inosine 5'-monophosphate and other purine nucleotides. [provided by RefSeq, Oct 2011]

OMIMResearchGenerating clinical summary…
DNmechanismARLOEUF 0.701 OMIM phenotype
Clinical SummaryNT5C2
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Gene-Disease Validity (ClinGen)
complex hereditary spastic paraplegia · ARDefinitive

Definitive — sufficient evidence for diagnostic panels

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

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Tolerant — LoF & missense variants common in population
LoF Constraint?
0.70LOEUF
pLI 0.000
Z-score 2.88
OE 0.46 (0.300.70)
Tolerant

Typical tolerance to LoF variation

Missense Constraint?
2.64Z-score
OE missense 0.58 (0.510.66)
181 obs / 312.5 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios?
LoF OE?0.46 (0.300.70)
00.351.4
Missense OE?0.58 (0.510.66)
00.61.4
Synonymous OE?1.09
01.21.6
LoF obs/exp: 15 / 32.8Missense obs/exp: 181 / 312.5Syn Z: -0.76

This gene — mechanism propensity

DN
0.6454th %ile
GOF
0.6149th %ile
LOF
0.2678th %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.

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

NT5C2 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

No active trials found for this gene.

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