PES1

pescadillo ribosomal biogenesis factor 1, the group of PeBoW complex

Basic information

Region (hg38): 22:30576625-30607083

Links

ENSG00000100029 ∙ NCBI:23481 ∙ OMIM:605819 ∙ HGNC:8848 ∙ Uniprot:O00541 ∙ 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 PES1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PES1 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			38	1		39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	38	1	1

Variants in PES1

This is a list of pathogenic ClinVar variants found in the PES1 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-30577088-C-T			Benign (May 08, 2018)
22-30578841-C-T		not specified	Uncertain significance (Jun 10, 2024)
22-30578892-C-T		not specified	Uncertain significance (Jan 27, 2022)
22-30579175-G-C		not specified	Uncertain significance (Jun 02, 2024)
22-30579235-C-T		not specified	Uncertain significance (Feb 05, 2024)
22-30579294-T-C		not specified	Uncertain significance (Jan 11, 2023)
22-30579758-C-A		not specified	Uncertain significance (Aug 17, 2021)
22-30579762-C-T		not specified	Uncertain significance (May 17, 2023)
22-30579765-C-T		not specified	Uncertain significance (Dec 02, 2022)
22-30579829-A-G		not specified	Uncertain significance (Nov 08, 2021)
22-30579877-C-T		not specified	Uncertain significance (May 05, 2023)
22-30580059-A-G		not specified	Uncertain significance (Jan 20, 2023)
22-30580108-G-A		not specified	Likely benign (Jan 03, 2024)
22-30580110-G-A		not specified	Uncertain significance (Feb 23, 2023)
22-30580134-C-A		not specified	Uncertain significance (Dec 20, 2023)
22-30580658-G-A		not specified	Uncertain significance (Mar 17, 2023)
22-30580691-G-A		not specified	Uncertain significance (May 23, 2024)
22-30581014-C-T		not specified	Uncertain significance (Oct 27, 2022)
22-30581027-C-G		not specified	Uncertain significance (Jun 11, 2021)
22-30581091-G-A		not specified	Uncertain significance (Apr 24, 2024)
22-30581360-C-T		not specified	Uncertain significance (Dec 02, 2022)
22-30581362-T-C		not specified	Uncertain significance (Sep 16, 2021)
22-30581405-C-T		not specified	Uncertain significance (Apr 13, 2022)
22-30581532-G-A		not specified	Uncertain significance (Dec 13, 2021)
22-30581565-C-T		not specified	Uncertain significance (Jun 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PES1	protein_coding	protein_coding	ENST00000354694	15	30459

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.719	0.281	125735	0	12	125747	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.31	301	372	0.809	0.0000241	3834
Missense in Polyphen		113	156.43	0.72235		1605
Synonymous	-0.0997	154	152	1.01	0.0000101	1117
Loss of Function	4.38	7	34.9	0.200	0.00000193	393

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000124	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000560	0.0000544
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000447	0.0000439
Middle Eastern	0.0000560	0.0000544
South Asian	0.0000994	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the PeBoW complex, which is required for maturation of 28S and 5.8S ribosomal RNAs and formation of the 60S ribosome. {ECO:0000255|HAMAP-Rule:MF_03028, ECO:0000269|PubMed:16738141, ECO:0000269|PubMed:17189298, ECO:0000269|PubMed:17353269}.

Recessive Scores

• pRec: 0.877

Intolerance Scores

• loftool: 0.571
• rvis_EVS: -0.13
• rvis_percentile_EVS: 44.03

Haploinsufficiency Scores

• pHI: 0.583
• hipred: Y
• hipred_score: 0.765
• ghis: 0.565

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.888

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pes1
• 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: pes
• Affected structure: radial glial cell
• Phenotype tag: abnormal
• Phenotype quality: disorganized

Gene ontology

• Biological process: maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA);maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA);rRNA processing;nucleolus organization;cell population proliferation;protein localization to organelle;ribosomal large subunit biogenesis;regulation of cell cycle
• Cellular component: condensed chromosome;nucleus;nucleoplasm;nucleolus;cytosol;membrane;preribosome, large subunit precursor;PeBoW complex
• Molecular function: RNA binding;protein binding;ribonucleoprotein complex binding