YPEL5

yippee like 5, the group of Yippee like family

Basic information

Region (hg38): 2:30146940-30160533

Links

ENSG00000119801 ∙ NCBI:51646 ∙ OMIM:609726 ∙ HGNC:18329 ∙ Uniprot:P62699 ∙ 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 YPEL5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the YPEL5 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			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	0	0

Variants in YPEL5

This is a list of pathogenic ClinVar variants found in the YPEL5 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-30156716-C-T		not specified	Uncertain significance (Jun 13, 2024)
2-30156728-A-G		not specified	Uncertain significance (Sep 13, 2023)
2-30158652-C-G		not specified	Uncertain significance (Dec 27, 2022)
2-30158707-A-G		not specified	Uncertain significance (Mar 16, 2022)
2-30158740-C-T		not specified	Uncertain significance (Feb 27, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
YPEL5	protein_coding	protein_coding	ENST00000379520	2	13593

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.465	0.512	125706	0	1	125707	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.29	22	79.4	0.277	0.00000516	793
Missense in Polyphen		2	22.816	0.087657		263
Synonymous	-0.757	32	27.0	1.19	0.00000146	242
Loss of Function	1.82	1	5.70	0.175	4.59e-7	47

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the CTLH E3 ubiquitin-protein ligase complex that selectively accepts ubiquitin from UBE2H and mediates ubiquitination and subsequent proteasomal degradation of the transcription factor HBP1 (PubMed:29911972). Required for normal cell proliferation (By similarity). {ECO:0000250|UniProtKB:Q65Z55, ECO:0000269|PubMed:29911972}.
• Pathway: Neutrophil degranulation;Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• rvis_EVS: 0.06
• rvis_percentile_EVS: 58

Haploinsufficiency Scores

• pHI: 0.377
• hipred: Y
• hipred_score: 0.593
• ghis: 0.575

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0559

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ypel5

Gene ontology

• Biological process: cell population proliferation;neutrophil degranulation
• Cellular component: ubiquitin ligase complex;extracellular region;nucleus;centrosome;midbody;mitotic spindle pole;tertiary granule lumen;ficolin-1-rich granule lumen
• Molecular function: protein binding;metal ion binding