ESF1

protein-coding

ESF1 nucleolar pre-rRNA processing protein homolog, the group of SSU processome

Gene summary

Enables RNA binding activity. Predicted to be involved in rRNA processing. Located in obsolete extracellular space. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C20orf6

MANE transcript

NM_001276380.2

Inheritance

—

ClinVar variants

U:103B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.28

Max pathogenic AF

—

Genomic locus

chr20:13,714,322-13,784,919

External References & Databases

Ensembl (ENSG00000089048)

Transcript & Mutation Effects

hg38 • Region Span ~70.6 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 ESF1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 103

not providedTotal: 5

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001276380.2. 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						0
missense			100 clinvar	8 clinvar		108
nonsense						0
start loss						0
frameshift				1 clinvar		1
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	103	9	0	112

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 28 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001276380.2	RefSeq	NP_001263309.1	13	MANE Select
ENST00000617257.2	Ensembl	ENSP00000480783.2	13	MANE Select
NM_016649.4	RefSeq	NP_057733.2	13	Standard
ENST00000202816.5	Ensembl	ENSP00000202816.1	13	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

rRNA processing

Molecular Function

RNA binding

Cellular Component

extracellular space
nucleoplasm
nucleolus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000202816
Coding exons: 13
Length: 70564
Individuals with no LoFs: 125696
Homozygous LoFs: 0
Heterozygous LoFs: 51
Defined: 125747
p: 0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.516	399	429	0.930	0.0000215	5763
Missense (PolyPhen)		155	180.98	0.85644		2502
Synonymous	-0.169	144	141	1.02	0.00000735	1361
Loss of Function	4.19	11	39.3	0.280	0.00000195	563

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00043	0.00043	rare
Latino/Admixed American	0.000089	0.000087	rare
Ashkenazi Jewish	0.00010	0.000099	rare
East Asian	0.00022	0.00022	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00020	0.00019	rare
South Asian	0.00040	0.00036	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May constitute a novel regulatory system for basal transcription. Negatively regulates ABT1 (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.0936

Intolerance Scores

LoFtool: 0.814
RVIS EVS: -0.69
RVIS percentile EVS: 15.27

Essentials

Essential (CRISPR): N
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: N
Indispensability score: 0.0208

Gene Damage Prediction

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