USP9X

Chr XXLRXLD

ubiquitin specific peptidase 9 X-linked

Also known as: DFFRX, FAF, FAF-X, FAM, MRX99, MRXS99F, XLID99, hFAM

The protein is a ubiquitin-specific protease that removes ubiquitin from target proteins in the cytoplasm. Loss-of-function mutations cause X-linked intellectual developmental disorder 99, which can present as either a syndromic female-restricted form or a non-syndromic form affecting both males and females. The inheritance pattern can be either X-linked recessive or X-linked dominant depending on the specific mutation and clinical presentation.

OMIMResearchSummary from RefSeq, OMIM, UniProt, Mechanism
LOFmechanismXLR/XLDLOEUF 0.052 OMIM phenotypes
Clinical SummaryUSP9X
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Gene-Disease Validity (ClinGen)
X-linked syndromic intellectual disability · XLDefinitive

Definitive — sufficient evidence for diagnostic panels

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.
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Clinical Trials
1 active or recruiting trial — potential therapeutic options may be available

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

Dual constrained — LoF & missense intolerant
LoF Constraint
0.05LOEUF
pLI 1.000
Z-score 8.86
OE 0.01 (0.000.05)
Highly constrained

Among the most LoF-intolerant genes (~top 3%)

Missense Constraint
6.41Z-score
OE missense 0.41 (0.370.44)
378 obs / 927.4 exp
Constrained

Extremely missense-constrained (top ~0.01%)

Observed / Expected Ratios
LoF OE0.01 (0.000.05)
00.351.4
Missense OE0.41 (0.370.44)
00.61.4
Synonymous OE0.97
01.21.6
LoF obs/exp: 1 / 93.5Missense obs/exp: 378 / 927.4Syn Z: 0.41
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
definitiveUSP9X-related intellectual developmental disorder (hemizygous)LOFXLR
strongUSP9X-related intellectual developmental disorder (heterozygous)LOFmonoallelic_X_heterozygous
DN
0.3594th %ile
GOF
0.5562th %ile
LOF
0.68top 25%

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

LOFprediction above median · LOEUF 0.05

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

USP9X · protein map & ClinVar variants

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

3D Protein StructureAlphaFold
Clinical Literature
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