ESF1

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

Basic information

Region (hg38): 20:13714322-13784919

Previous symbols: [ "C20orf6" ]

Links

ENSG00000089048 ∙ NCBI:51575 ∙ OMIM:618765 ∙ HGNC:15898 ∙ Uniprot:Q9H501 ∙ 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 ESF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ESF1 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			38	5		43
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				4	1	5
Total	0	0	38	10	1

Variants in ESF1

This is a list of pathogenic ClinVar variants found in the ESF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-13714909-GCT-G			Likely benign (Jun 06, 2018)
20-13714927-T-C		not specified	Likely benign (Oct 26, 2022)
20-13714978-C-T		not specified	Uncertain significance (Dec 21, 2022)
20-13715026-G-C		not specified	Uncertain significance (Nov 17, 2022)
20-13715031-T-C		not specified	Uncertain significance (Jul 06, 2021)
20-13715117-G-C		not specified	Uncertain significance (Apr 25, 2023)
20-13717378-T-C		not specified	Uncertain significance (Aug 04, 2023)
20-13718969-G-A		not specified	Uncertain significance (Aug 02, 2022)
20-13728465-C-A		not specified	Uncertain significance (Aug 09, 2021)
20-13733757-C-A		not specified	Uncertain significance (Oct 03, 2023)
20-13733780-G-A		not specified	Uncertain significance (Apr 20, 2023)
20-13733818-A-G		not specified	Uncertain significance (May 17, 2023)
20-13759718-A-G		not specified	Uncertain significance (Nov 14, 2023)
20-13759800-C-G		not specified	Uncertain significance (Jan 18, 2023)
20-13759853-C-T		not specified	Uncertain significance (Jan 23, 2023)
20-13766832-T-G		not specified	Uncertain significance (May 24, 2023)
20-13766843-T-C		not specified	Uncertain significance (Apr 22, 2022)
20-13766896-T-A		not specified	Uncertain significance (Jan 17, 2023)
20-13769960-A-T		not specified	Uncertain significance (Nov 27, 2023)
20-13775162-C-T		not specified	Likely benign (Oct 04, 2022)
20-13775211-C-A		not specified	Uncertain significance (Apr 19, 2024)
20-13775260-C-T		not specified	Uncertain significance (Sep 14, 2022)
20-13775263-C-T		not specified	Likely benign (Aug 26, 2022)
20-13775876-A-C		not specified	Uncertain significance (Oct 26, 2021)
20-13775883-C-T		not specified	Uncertain significance (Mar 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ESF1	protein_coding	protein_coding	ENST00000202816	13	70564

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0178	0.982	125696	0	51	125747	0.000203

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.516	399	429	0.930	0.0000215	5763
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000522	0.000520
Ashkenazi Jewish	0.000102	0.0000992
East Asian	0.000225	0.000217
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000203	0.000193
Middle Eastern	0.000225	0.000217
South Asian	0.000396	0.000359
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.657
• hipred: Y
• hipred_score: 0.696
• ghis: 0.619

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0208

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Esf1

Gene ontology

• Biological process: rRNA processing
• Cellular component: extracellular space;nucleoplasm;nucleolus
• Molecular function: RNA binding