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.

not_specified (80 variants)
not_provided (1 variants)
EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)

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. These statistics are base on transcript: NM_000014303.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar		1 clinvar	2
missense			81 clinvar	2 clinvar		83
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	86	2	1

Loading clinvar variants...

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