YPEL3

yippee like 3, the group of Yippee like family

Basic information

Region (hg38): 16:30092314-30096915

Links

ENSG00000090238 ∙ NCBI:83719 ∙ OMIM:609724 ∙ HGNC:18327 ∙ Uniprot:P61236 ∙ 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 YPEL3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the YPEL3 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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	0

Variants in YPEL3

This is a list of pathogenic ClinVar variants found in the YPEL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-30094872-C-T		not specified	Uncertain significance (Mar 11, 2022)
16-30095136-C-T		not specified	Uncertain significance (Jul 14, 2023)
16-30095311-T-C		not specified	Uncertain significance (Nov 07, 2023)
16-30095362-G-A		not specified	Uncertain significance (Jul 12, 2023)
16-30095374-G-T		not specified	Uncertain significance (Dec 16, 2021)
16-30095419-A-G		not specified	Uncertain significance (Apr 06, 2024)
16-30095460-G-A		not specified	Uncertain significance (Sep 11, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
YPEL3	protein_coding	protein_coding	ENST00000398841	4	4602

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0416	0.855	125029	0	4	125033	0.0000160

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.54	59	103	0.573	0.00000655	1024
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000952	0.0000927
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000181	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.347
• hipred: N
• hipred_score: 0.272
• ghis: 0.616

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ypel3
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); skeleton phenotype; limbs/digits/tail phenotype

Zebrafish Information Network

• Gene name: ypel3
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: decreased length

Gene ontology

• Biological process: positive regulation of cellular senescence
• Cellular component: nucleolus
• Molecular function: metal ion binding