FCF1

FCF1 rRNA-processing protein, the group of SSU processome|Endoribonucleases

Basic information

Region (hg38): 14:74713143-74738620

Previous symbols: [ "C14orf111" ]

Links

ENSG00000119616 ∙ NCBI:51077 ∙ ∙ HGNC:20220 ∙ Uniprot:Q9Y324 ∙ 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 FCF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FCF1 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			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	10	0	0

Variants in FCF1

This is a list of pathogenic ClinVar variants found in the FCF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-74713536-C-G		not specified	Uncertain significance (May 18, 2023)
14-74713546-A-G		not specified	Uncertain significance (Jan 18, 2023)
14-74714942-G-A		not specified	Uncertain significance (Jan 05, 2022)
14-74715951-T-C		not specified	Likely benign (Dec 30, 2023)
14-74716018-G-A		not specified	Uncertain significance (Oct 05, 2021)
14-74716025-C-G		not specified	Uncertain significance (Sep 20, 2023)
14-74716066-G-A		not specified	Uncertain significance (Oct 12, 2022)
14-74716091-A-G		not specified	Uncertain significance (Nov 09, 2023)
14-74723277-C-T		not specified	Uncertain significance (Mar 07, 2024)
14-74723308-T-C		not specified	Uncertain significance (May 08, 2024)
14-74732754-A-G		not specified	Uncertain significance (Nov 06, 2023)
14-74734077-A-G		not specified	Uncertain significance (Feb 13, 2024)
14-74734136-C-A		not specified	Uncertain significance (Jun 11, 2024)
14-74734911-A-T		not specified	Uncertain significance (May 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FCF1	protein_coding	protein_coding	ENST00000341162	8	23548

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0244	0.963	125729	0	12	125741	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.893	82	108	0.758	0.00000558	1296
Missense in Polyphen		10	15.188	0.65843		201
Synonymous	0.568	31	35.3	0.878	0.00000174	337
Loss of Function	2.19	5	13.8	0.363	7.43e-7	174

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000578	0.0000578
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000617	0.0000615
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Essential protein involved in pre-rRNA processing and 40S ribosomal subunit assembly. {ECO:0000250}.
• Pathway: Ribosome biogenesis in eukaryotes - Homo sapiens (human);rRNA processing;Metabolism of RNA;rRNA modification in the nucleus and cytosol;rRNA processing in the nucleus and cytosol (Consensus)

Recessive Scores

• pRec: 0.136

Intolerance Scores

• loftool: 0.398
• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.76

Haploinsufficiency Scores

• pHI: 0.205
• hipred: Y
• hipred_score: 0.595
• ghis: 0.622

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.567

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fcf1

Gene ontology

• Biological process: rRNA processing
• Cellular component: nucleoplasm;nucleolus;small-subunit processome
• Molecular function: RNA binding