FBL

fibrillarin, the group of 7BS 2'O-ribose DNA/RNA methyltransferases|U3 small nucleolar ribonucleoprotein

Basic information

Region (hg38): 19:39834458-39846379

Links

ENSG00000105202 ∙ NCBI:2091 ∙ OMIM:134795 ∙ HGNC:3599 ∙ Uniprot:P22087 ∙ 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 FBL gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FBL 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					1	1
missense			24			24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	0	1

Variants in FBL

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

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

Position	Type	Phenotype	Significance	ClinVar
19-39836596-G-A		not specified	Uncertain significance (Sep 28, 2022)
19-39837722-C-T		not specified	Uncertain significance (Mar 22, 2023)
19-39837800-C-T		not specified	Uncertain significance (Mar 06, 2023)
19-39839036-G-A		not specified	Uncertain significance (Mar 17, 2023)
19-39839042-A-G		not specified	Uncertain significance (Nov 08, 2024)
19-39839103-C-T		not specified	Uncertain significance (Feb 11, 2022)
19-39839108-G-A		not specified	Uncertain significance (Oct 28, 2024)
19-39839111-T-C		not specified	Uncertain significance (Dec 28, 2023)
19-39840419-T-C		not specified	Uncertain significance (Mar 18, 2024)
19-39840437-A-G		not specified	Uncertain significance (Aug 10, 2024)
19-39840452-G-A		not specified	Uncertain significance (Jul 22, 2024)
19-39840471-C-T		not specified	Uncertain significance (Oct 24, 2024)
19-39840476-C-G		not specified	Uncertain significance (Feb 27, 2025)
19-39840489-G-C		not specified	Uncertain significance (May 13, 2024)
19-39840619-C-T		not specified	Uncertain significance (Feb 17, 2024)
19-39840623-T-C		not specified	Likely benign (Feb 27, 2025)
19-39840635-C-T		not specified	Uncertain significance (Jul 21, 2021)
19-39840638-C-T		not specified	Uncertain significance (Mar 31, 2023)
19-39840671-G-A		not specified	Uncertain significance (Aug 07, 2024)
19-39840691-C-G		not specified	Uncertain significance (Nov 13, 2023)
19-39840712-C-G		not specified	Uncertain significance (Jan 23, 2024)
19-39840722-C-G		not specified	Uncertain significance (Jul 30, 2023)
19-39840737-G-A		not specified	Uncertain significance (May 17, 2023)
19-39840751-C-A		not specified	Uncertain significance (Dec 22, 2023)
19-39840751-C-T		not specified	Uncertain significance (Nov 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FBL	protein_coding	protein_coding	ENST00000221801	9	11957

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.993	0.00681	125707	0	3	125710	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.20	160	209	0.767	0.0000135	2024
Missense in Polyphen		27	56.645	0.47665		646
Synonymous	0.449	75	80.1	0.936	0.00000514	688
Loss of Function	3.86	1	19.3	0.0519	0.00000131	191

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000619	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000886	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: S-adenosyl-L-methionine-dependent methyltransferase that has the ability to methylate both RNAs and proteins. Involved in pre-rRNA processing by catalyzing the site-specific 2'-hydroxyl methylation of ribose moieties in pre-ribosomal RNA. Site specificity is provided by a guide RNA that base pairs with the substrate. Methylation occurs at a characteristic distance from the sequence involved in base pairing with the guide RNA. Also acts as a protein methyltransferase by mediating methylation of 'Gln-105' of histone H2A (H2AQ104me), a modification that impairs binding of the FACT complex and is specifically present at 35S ribosomal DNA locus (PubMed:24352239). {ECO:0000269|PubMed:24352239}.
• Pathway: Ribosome biogenesis in eukaryotes - Homo sapiens (human);rRNA processing;Metabolism of RNA;TNFalpha;rRNA modification in the nucleus and cytosol;rRNA processing in the nucleus and cytosol (Consensus)

Intolerance Scores

• loftool: 0.137
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.66

Haploinsufficiency Scores

• pHI: 0.952
• hipred: Y
• hipred_score: 0.840
• ghis: 0.612

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.976

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fbl
• Phenotype: embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Zebrafish Information Network

• Gene name: fbl
• Affected structure: trunk
• Phenotype tag: abnormal
• Phenotype quality: decreased thickness

Gene ontology

• Biological process: box C/D snoRNA 3'-end processing;osteoblast differentiation;rRNA processing;rRNA methylation;snoRNA localization;histone glutamine methylation
• Cellular component: fibrillar center;dense fibrillar component;granular component;nucleus;nucleoplasm;chromosome;nucleolus;Cajal body;membrane;box C/D snoRNP complex;small-subunit processome;extracellular exosome
• Molecular function: TFIID-class transcription factor complex binding;RNA binding;protein binding;rRNA methyltransferase activity;ATPase binding;histone-glutamine methyltransferase activity