NUTF2

Chr 16

nuclear transport factor 2

Also known as: NTF-2, NTF2, PP15

NCBI Gene: 10204 ENSG00000102898 UniProt: P61970

This gene encodes a cytosolic factor that facilitates protein transport into the nucleus. The encoded protein is required for nuclear import of the small Ras-like GTPase, Ran which is involved in numerous cellular processes. This protein also interacts with the nuclear pore complex glycoprotein p62. [provided by RefSeq, Apr 2016]

Active trials

Pathogenic / LP

ClinVar variants

Pubs (1 yr)

2.3

Missense Z

0.34

LOEUF· LoF intolerant

Clinical Summary— NUTF2

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Population Constraint (gnomAD)

Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 0.94). One damaged copy is likely sufficient to cause disease.

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

LoF intolerant — likely haploinsufficient

LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.

0.34LOEUF

pLI 0.939

Z-score 2.76

OE 0.00 (0.00–0.34)

Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.

2.29Z-score

OE missense 0.25 (0.18–0.37)

19 obs / 74.6 exp

Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.

LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.00 (0.00–0.34)

0≤0.351.4

Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.25 (0.18–0.37)

0≤0.61.4

Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.0.99

0≤1.21.6

LoF obs/exp: 0 / 8.9Missense obs/exp: 19 / 74.6Syn Z: 0.06

0.3991th %ile

GOF

0.3690th %ile

LOF

0.68top 25%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOFprediction above median · LOEUF 0.34

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.