FCF1

protein-coding

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

Gene summary

Enables RNA binding activity. Involved in ribosomal small subunit biogenesis. Part of small-subunit processome. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C14orf111

MANE transcript

NM_015962.5

Inheritance

—

ClinVar variants

U:27B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.36

Max pathogenic AF

—

Genomic locus

chr14:74,713,144-74,738,620

External References & Databases

Ensembl (ENSG00000119616)

Transcript & Mutation Effects

hg38 • Region Span ~25.5 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 FCF1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 23

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_015962.5. 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 clinvar		2
missense			24 clinvar			24
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	27	1	0	28

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 19 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_015962.5	RefSeq	NP_057046.1	8	MANE Select
ENST00000341162.8	Ensembl	ENSP00000344393.4	8	MANE Select
NM_001318508.2	RefSeq	NP_001305437.1	7	Standard
ENST00000534938.6	Ensembl	ENSP00000444939.2	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

rRNA processing

Molecular Function

RNA binding

Cellular Component

nucleoplasm
nucleolus
small-subunit processome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000341162
Coding exons: 8
Length: 23548
Individuals with no LoFs: 125729
Homozygous LoFs: 0
Heterozygous LoFs: 12
Defined: 125741
p: 0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.893	82	108	0.758	0.00000558	1296
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000062	0.000062	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Essential protein involved in pre-rRNA processing and 40S ribosomal subunit assembly. {ECO:0000250}.;

Recessive Scores

pRec: 0.136

Intolerance Scores

LoFtool: 0.398
RVIS EVS: -0.05
RVIS percentile EVS: 49.76

Essentials

Essential (CRISPR): N
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.567

Gene Damage Prediction

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