FTSJ3

protein-coding

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

Gene summary

Although the function of this gene is not known, the existence of this gene is supported by mRNA and EST data. A possible function of the encoded protein can be inferred from amino acid sequence similarity to the E.coli FtsJ protein and to a mouse protein possibly involved in embryogenesis. [provided by RefSeq, Jul 2008]

MANE transcript

NM_017647.4

Inheritance

—

ClinVar variants

U:177B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.26

Max pathogenic AF

—

Genomic locus

chr17:63,819,433-63,830,012

External References & Databases

Ensembl (ENSG00000108592)

Transcript & Mutation Effects

hg38 • Region Span ~10.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to FTSJ3 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 162

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017647.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			163 clinvar	6 clinvar		169
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			12 clinvar			12
Total	0	0	177	6	0	183

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 14 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017647.4	RefSeq	NP_060117.3	20	MANE Select
ENST00000427159.7	Ensembl	ENSP00000396673.2	20	MANE Select
ENST00000579569.5	Ensembl	ENSP00000462342.1	3	Standard
ENST00000579831.1	Ensembl	ENSP00000462212.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

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

Molecular Function

RNA binding
protein binding
rRNA (uridine-2'-O-)-methyltransferase activity
rRNA (guanine) methyltransferase activity

Cellular Component

nucleus
nucleolus
preribosome, large subunit precursor
preribosome, small subunit precursor

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000427159
Coding exons: 20
Length: 10580
Individuals with no LoFs: 125706
Homozygous LoFs: 0
Heterozygous LoFs: 42
Defined: 125748
p: 0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.423	518	492	1.05	0.0000299	5532
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00037	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00027	0.00027	rare
Finnish	0.00018	0.00018	rare
European (Non-Finnish)	0.00014	0.00014	rare
South Asian	0.00030	0.00023	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.860

Gene Damage Prediction

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