YPEL4

protein-coding

yippee like 4, the group of Yippee like family

Gene summary

Predicted to enable metal ion binding activity. Predicted to act upstream of or within several processes, including negative regulation of erythrocyte clearance; negative regulation of erythrocyte differentiation; and protein localization to plasma membrane. Predicted to be located in nucleolus. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_145008.3

Inheritance

—

ClinVar variants

U:13

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.3

Max pathogenic AF

—

Genomic locus

chr11:57,645,087-57,649,944

External References & Databases

Ensembl (ENSG00000166793)

Transcript & Mutation Effects

hg38 • Region Span ~4.9 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 YPEL4 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 12

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_145008.3. 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			1 clinvar			1
missense			12 clinvar			12
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	13	0	0	13

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_145008.3	RefSeq	NP_659445.1	4	MANE Select
ENST00000300022.8	Ensembl	ENSP00000300022.3	4	MANE Select
NM_001363487.2	RefSeq	NP_001350416.1	4	Standard
ENST00000524669.5	Ensembl	ENSP00000432648.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

metal ion binding

Cellular Component

nucleolus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000524669
Coding exons: 4
Length: 4858
Individuals with no LoFs: 125737
Homozygous LoFs: 0
Heterozygous LoFs: 4
Defined: 125741
p: 0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.33	38	69.0	0.551	0.00000347	826
Missense (PolyPhen)		10	31.376	0.31871		374
Synonymous	0.759	21	25.9	0.810	0.00000147	226
Loss of Function	1.69	2	6.73	0.297	3.37e-7	79

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00014	0.00012	rare
Latino/Admixed American	0	0.0	absent
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

Recessive Scores

pRec: 0.113

Intolerance Scores

LoFtool: 0.248
RVIS EVS: -0.01
RVIS percentile EVS: 52.85

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.700

Gene Damage Prediction

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