ZFX

Chr XX-linked

zinc finger protein X-linked

ZFX encodes a transcriptional activator containing 13 zinc fingers that regulates stem cell self-renewal in hematopoietic and other tissues. Mutations cause X-linked syndromic intellectual developmental disorder 37. The gene is highly constrained against loss-of-function variants (pLI = 1.0, LOEUF = 0.16), indicating intolerance to functional disruption.

OMIMResearchSummary from RefSeq, OMIM, UniProt
LOFmechanismX-linkedLOEUF 0.161 OMIM phenotype
Clinical SummaryZFX
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Gene-Disease Validity (ClinGen)
X-linked syndromic complex neurodevelopmental disorder · XLStrong

Strong evidence — appropriate for clinical testing

Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 1.00). One damaged copy is likely sufficient to cause disease.
Some data sources returned errors (1)

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Dual constrained — LoF & missense intolerant
LoF Constraint
0.16LOEUF
pLI 0.998
Z-score 4.00
OE 0.00 (0.000.16)
Highly constrained

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

Missense Constraint
3.15Z-score
OE missense 0.50 (0.440.57)
158 obs / 315.2 exp
Constrained

Highly missense-constrained (top ~0.1%)

Observed / Expected Ratios
LoF OE0.00 (0.000.16)
00.351.4
Missense OE0.50 (0.440.57)
00.61.4
Synonymous OE1.01
01.21.6
LoF obs/exp: 0 / 18.6Missense obs/exp: 158 / 315.2Syn Z: -0.08
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
moderateZFX-related neurodevelopmental disorder with hypotonia, congenital anomalies and facial dysmorphism with or without hyperparathyroidismLOFmonoallelic_X_heterozygous
DN
0.3594th %ile
GOF
0.3094th %ile
LOF
0.81top 5%

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

LOFprediction above median · LOEUF 0.16

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

ClinVar Variant Classifications

0 submitted variants in ClinVar

Protein Context — Lollipop Plot

ZFX · protein map & ClinVar variants

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

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

No active trials found for this gene.

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Clinical Literature
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