FTSJ3

FtsJ RNA 2'-O-methyltransferase 3, the group of Armadillo like helical domain containing|7BS 2'O-ribose DNA/RNA methyltransferases

Basic information

Region (hg38): 17:63819433-63830012

Links

ENSG00000108592 ∙ NCBI:117246 ∙ OMIM:618411 ∙ HGNC:17136 ∙ Uniprot:Q8IY81 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FTSJ3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FTSJ3 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						0
missense			83	3		86
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	83	3	0

Variants in FTSJ3

This is a list of pathogenic ClinVar variants found in the FTSJ3 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-63819809-C-G		not specified	Uncertain significance (Jan 07, 2025)
17-63819812-T-G		not specified	Uncertain significance (Jan 21, 2025)
17-63819836-C-T		not specified	Uncertain significance (Jan 06, 2023)
17-63819851-T-C		not specified	Uncertain significance (May 29, 2024)
17-63819890-C-T		not specified	Uncertain significance (Jan 24, 2024)
17-63819911-C-T		not specified	Uncertain significance (Feb 16, 2023)
17-63819912-G-A		not specified	Uncertain significance (Dec 01, 2022)
17-63819921-G-A		not specified	Uncertain significance (Dec 06, 2023)
17-63819929-C-T		not specified	Uncertain significance (Mar 27, 2023)
17-63819938-G-A		not specified	Uncertain significance (Mar 29, 2023)
17-63819983-T-G		not specified	Uncertain significance (Jun 24, 2022)
17-63819984-T-C		not specified	Uncertain significance (Jun 24, 2022)
17-63820099-C-A		not specified	Uncertain significance (Nov 17, 2022)
17-63820103-C-T		not specified	Uncertain significance (Dec 03, 2021)
17-63820127-A-G		not specified	Uncertain significance (Feb 25, 2025)
17-63820131-C-T		not specified	Uncertain significance (Mar 25, 2024)
17-63820301-C-T		not specified	Uncertain significance (Nov 02, 2023)
17-63820317-G-A		not specified	Uncertain significance (Jan 18, 2025)
17-63820323-G-A		not specified	Uncertain significance (Dec 04, 2024)
17-63820341-C-A		not specified	Uncertain significance (Oct 03, 2024)
17-63820367-C-T		not specified	Uncertain significance (Apr 29, 2024)
17-63820373-C-T		not specified	Uncertain significance (Jun 10, 2024)
17-63820374-G-A		not specified	Uncertain significance (Feb 28, 2025)
17-63820415-C-T		not specified	Uncertain significance (Jul 30, 2023)
17-63820418-T-C		not specified	Uncertain significance (Oct 22, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FTSJ3	protein_coding	protein_coding	ENST00000427159	20	10580

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0372	0.963	125706	0	42	125748	0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.423	518	492	1.05	0.0000299	5532
Missense in Polyphen		181	200.43	0.90306		2333
Synonymous	-1.41	201	177	1.13	0.00000943	1632
Loss of Function	4.86	13	50.2	0.259	0.00000283	553

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000486	0.000486
Ashkenazi Jewish	0.00	0.00
East Asian	0.000273	0.000272
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000142	0.000141
Middle Eastern	0.000273	0.000272
South Asian	0.000296	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable methyltransferase involved in the processing of the 34S pre-rRNA to 18S rRNA and in 40S ribosomal subunit formation. {ECO:0000255|HAMAP-Rule:MF_03163, ECO:0000269|PubMed:22195017}.

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.695
• rvis_EVS: 0.07
• rvis_percentile_EVS: 59.16

Haploinsufficiency Scores

• pHI: 0.125
• hipred: N
• hipred_score: 0.414
• ghis: 0.539

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.860

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ftsj3

Gene ontology

• Biological process: enzyme-directed rRNA 2'-O-methylation;maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA);maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA);rRNA methylation
• Cellular component: nucleus;nucleolus;preribosome, large subunit precursor;preribosome, small subunit precursor
• Molecular function: RNA binding;protein binding;rRNA (uridine-2'-O-)-methyltransferase activity;rRNA (guanine) methyltransferase activity