YPEL5

protein-coding

yippee like 5, the group of Yippee like family

Gene summary

Predicted to enable metal ion binding activity. Predicted to be involved in cell population proliferation. Part of ubiquitin ligase complex. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_016061.3

Inheritance

—

ClinVar variants

U:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.18

Max pathogenic AF

—

Genomic locus

chr2:30,146,941-30,160,537

External References & Databases

Ensembl (ENSG00000119801)

Transcript & Mutation Effects

hg38 • Region Span ~13.6 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 YPEL5 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 8

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016061.3. 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			9 clinvar			9
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	9	0	0	9

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 86 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016061.3	RefSeq	NP_057145.1	2	MANE Select
ENST00000261353.9	Ensembl	ENSP00000261353.4	2	MANE Select
NM_001127399.2	RefSeq	NP_001120871.1	2	Standard
NM_001127400.2	RefSeq	NP_001120872.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Neutrophil degranulation
Innate Immune System
Immune System

Biological Process

cell population proliferation
neutrophil degranulation

Molecular Function

protein binding
metal ion binding

Cellular Component

ubiquitin ligase complex
extracellular region
nucleus
centrosome
midbody

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000379520
Coding exons: 2
Length: 13593
Individuals with no LoFs: 125706
Homozygous LoFs: 0
Heterozygous LoFs: 1
Defined: 125707
p: 0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.29	22	79.4	0.277	0.00000516	793
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.113

Intolerance Scores

RVIS EVS: 0.06
RVIS percentile EVS: 58

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): E
Indispensability pred.: N
Indispensability score: 0.0559

Gene Damage Prediction

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