YPEL3

protein-coding

yippee like 3, the group of Yippee like family

Gene summary

Predicted to enable metal ion binding activity. Involved in positive regulation of cellular senescence. Predicted to be located in nucleolus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_031477.5

Inheritance

—

ClinVar variants

P:1U:12

Top phenotype

YPEL3-related condition

gnomAD constraint

pLI —, LoF o/e 0.45

Max pathogenic AF

—

Genomic locus

chr16:30,092,314-30,096,915

External References & Databases

Ensembl (ENSG00000090238)

Transcript & Mutation Effects

hg38 • Region Span ~4.6 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 YPEL3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 10

YPEL3-related conditionTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_031477.5. 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			1 clinvar			1
missense			11 clinvar			11
nonsense						0
start loss						0
frameshift	1 clinvar					1
splice donor/acceptor (+/-2bp)						0
Total	1	0	12	0	0	13

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 19 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_031477.5	RefSeq	NP_113665.3	4	MANE Select
ENST00000398841.6	Ensembl	ENSP00000381821.1	4	MANE Select
NM_001145524.2	RefSeq	NP_001138996.1	4	Standard
ENST00000398838.8	Ensembl	ENSP00000381818.4	4	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
ypel3	Danio rerio	Structure: post-vent region Quality: decreased length abnormal

Gene / Model

Organism

Observed Phenotype

ypel3

Danio rerio

Structure: post-vent region

Quality: decreased length

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

positive regulation of cellular senescence

Molecular Function

metal ion binding

Cellular Component

nucleolus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000398841
Coding exons: 4
Length: 4602
Individuals with no LoFs: 125029
Homozygous LoFs: 0
Heterozygous LoFs: 4
Defined: 125033
p: 0.0000160

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.54	59	103	0.573	0.00000655	1024
Missense (PolyPhen)		18	41.231	0.43657		399
Synonymous	0.120	43	44.0	0.977	0.00000303	307
Loss of Function	1.32	3	6.70	0.448	2.84e-7	78

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000066	0.000064	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in proliferation and apoptosis in myeloid precursor cells. {ECO:0000250}.;

Recessive Scores

pRec: 0.113

Intolerance Scores

LoFtool: 0.289
RVIS EVS: 0.19
RVIS percentile EVS: 66.57

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.231

Gene Damage Prediction

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