FTSJ1

Chr XXLR

FtsJ RNA 2'-O-methyltransferase 1

Also known as: CDLIV, JM23, MRX44, MRX9, SPB1, TRMT7, XLID9

This highly constrained gene encodes a methyltransferase that modifies specific nucleotides in the anticodon loop of tRNAs, which is essential for accurate protein synthesis. Mutations cause X-linked intellectual developmental disorder, with males affected due to X-linked recessive inheritance. The protein's critical role in cytoplasmic translation and neurogenesis explains the neurodevelopmental phenotype observed in affected individuals.

Summary from RefSeq, OMIM, UniProt
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Primary Disease Associations & Inheritance

Intellectual developmental disorder, X-linked 9MIM #309549
XLR
0
Active trials
6
Pubs (1 yr)
0
P/LP submissions
P/LP missense
0.20
LOEUF· LoF intol.
LOF
Mechanism· G2P
Clinical SummaryFTSJ1
🧬
Gene-Disease Validity (ClinGen)
X-linked complex neurodevelopmental disorder · 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 0.99). One damaged copy is likely sufficient to cause disease.
Some data sources returned errors (1)

pubtator: TimeoutError: The operation was aborted due to timeout

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

LoF intolerant — likely haploinsufficient
LoF Constraint
0.20LOEUF
pLI 0.993
Z-score 3.54
OE 0.00 (0.000.20)
Highly constrained

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

Missense Constraint
2.17Z-score
OE missense 0.50 (0.410.60)
73 obs / 147.1 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios
LoF OE0.00 (0.000.20)
00.351.4
Missense OE0.50 (0.410.60)
00.61.4
Synonymous OE0.92
01.21.6
LoF obs/exp: 0 / 14.6Missense obs/exp: 73 / 147.1Syn Z: 0.46
Curated Mechanism (G2P)Gene2Phenotype (DDG2P) ↗
definitiveFTSJ1-related intellectual developmental disorderLOFXLR
DN
0.3296th %ile
GOF
0.3392th %ile
LOF
0.69top 10%

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

LOFprediction above median · LOEUF 0.20

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

FTSJ1 · 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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