FTSJ1

FtsJ RNA 2'-O-methyltransferase 1, the group of 7BS 2'O-ribose DNA/RNA methyltransferases

Basic information

Region (hg38): X:48476021-48486364

Previous symbols: [ "MRX9", "MRX44" ]

Links

ENSG00000068438 ∙ NCBI:24140 ∙ OMIM:300499 ∙ HGNC:13254 ∙ Uniprot:Q9UET6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual disability, X-linked 9 (Strong), mode of inheritance: XL
• non-syndromic X-linked intellectual disability (Supportive), mode of inheritance: XL
• X-linked complex neurodevelopmental disorder (Definitive), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual developmental disorder, X-linked 9	XL	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	8288232; 10398246; 12239714; 15162322; 15342698; 18081026

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FTSJ1 gene.

• Inborn genetic diseases (3 variants)
• not provided (2 variants)
• Intellectual disability (1 variants)
• Intellectual disability, X-linked 9 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FTSJ1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			2	8	4	14
missense	2	1	31	4	3	41
nonsense						0
start loss						0
frameshift	3	1				4
inframe indel						0
splice donor/acceptor (+/-2bp)	1					1
splice region			3	3	2	8
non coding			1	1	4	6
Total	6	2	34	13	11

Variants in FTSJ1

This is a list of pathogenic ClinVar variants found in the FTSJ1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
X-48478019-G-A			Likely benign (Feb 01, 2025)
X-48478081-T-A		Inborn genetic diseases	Pathogenic (Jul 27, 2013)
X-48478103-ATGGC-A			Pathogenic (Dec 12, 2019)
X-48478117-C-T		Intellectual disability, X-linked 9	Uncertain significance (Feb 02, 2024)
X-48478122-C-T		Inborn genetic diseases	Likely benign (May 01, 2018)
X-48478158-A-C		Inborn genetic diseases	Uncertain significance (Jun 02, 2023)
X-48478167-AG-A		Intellectual disability, X-linked 9	Pathogenic (Aug 01, 2004)
X-48478177-C-G			Likely benign (Dec 31, 2019)
X-48478443-G-C			Uncertain significance (Feb 14, 2024)
X-48478457-CG-C		Inborn genetic diseases	Pathogenic (Nov 23, 2022)
X-48478488-G-C		Inborn genetic diseases	Likely pathogenic (Mar 27, 2015)
X-48478514-A-G		Inborn genetic diseases	Uncertain significance (Aug 22, 2016)
X-48478516-C-G			Uncertain significance (Feb 17, 2023)
X-48478517-G-A			Benign (Jun 16, 2018)
X-48478577-G-A			Benign (Jun 21, 2021)
X-48478615-A-G		Intellectual disability, X-linked 9	Pathogenic (Sep 01, 2004)
X-48478618-G-A		Inborn genetic diseases	Uncertain significance (Sep 22, 2023)
X-48478621-C-T		Intellectual disability, X-linked 9	Pathogenic (Aug 01, 2004)
X-48478629-C-T		Inborn genetic diseases	Likely benign (Dec 30, 2019)
X-48478630-G-A		Inborn genetic diseases	Uncertain significance (Mar 06, 2018)
X-48478630-G-T		History of neurodevelopmental disorder	Uncertain significance (Mar 01, 2017)
X-48478666-C-G			Uncertain significance (Jan 15, 2021)
X-48478679-TG-T		Intellectual disability, X-linked 9	Pathogenic (Jan 01, 2019)
X-48478695-G-T		not specified • Inborn genetic diseases	Benign (Dec 31, 2019)
X-48478698-C-T			Likely benign (Jun 08, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FTSJ1	protein_coding	protein_coding	ENST00000348411	11	10212

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.993	0.00746	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.17	73	147	0.496	0.0000126	2137
Missense in Polyphen		8	51.464	0.15545		703
Synonymous	0.460	55	59.5	0.924	0.00000504	659
Loss of Function	3.54	0	14.6	0.00	0.00000109	221

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Methylates the 2'-O-ribose of nucleotides at positions 32 and 34 of the tRNA anticodon loop of substrate tRNAs. {ECO:0000255|HAMAP-Rule:MF_03162}.
• Pathway: tRNA modification in the nucleus and cytosol;tRNA processing;Metabolism of RNA (Consensus)

Recessive Scores

• pRec: 0.177

Intolerance Scores

• rvis_EVS: -0.01
• rvis_percentile_EVS: 53.51

Haploinsufficiency Scores

• pHI: 0.0644
• hipred: Y
• hipred_score: 0.642
• ghis: 0.542

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Ftsj1
• Phenotype: normal phenotype; vision/eye phenotype; hearing/vestibular/ear phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: tRNA nucleoside ribose methylation;cytoplasmic translation;tRNA modification;tRNA methylation
• Cellular component: cytoplasm;cytosol
• Molecular function: tRNA methyltransferase activity;tRNA (guanosine-2'-O-)-methyltransferase activity;tRNA (cytosine-2'-O-)-methyltransferase activity