YPEL4

yippee like 4, the group of Yippee like family

Basic information

Region (hg38): 11:57645087-57649944

Links

ENSG00000166793 ∙ NCBI:219539 ∙ OMIM:609725 ∙ HGNC:18328 ∙ Uniprot:Q96NS1 ∙ 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 YPEL4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the YPEL4 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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	0

Variants in YPEL4

This is a list of pathogenic ClinVar variants found in the YPEL4 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-57646327-C-G		not specified	Uncertain significance (May 24, 2024)
11-57646349-G-A		not specified	Uncertain significance (Feb 23, 2023)
11-57646395-C-T		not specified	Uncertain significance (Feb 22, 2024)
11-57646399-G-C		not specified	Uncertain significance (Dec 09, 2024)
11-57647011-G-A		not specified	Uncertain significance (Oct 02, 2023)
11-57647038-G-A		not specified	Uncertain significance (Aug 22, 2023)
11-57647089-C-T		not specified	Uncertain significance (Nov 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
YPEL4	protein_coding	protein_coding	ENST00000524669	4	4858

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.196	0.762	125737	0	4	125741	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.33	38	69.0	0.551	0.00000347	826
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000141	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.248
• rvis_EVS: -0.01
• rvis_percentile_EVS: 52.85

Haploinsufficiency Scores

• pHI: 0.302
• hipred: Y
• hipred_score: 0.529
• ghis: 0.653

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.700

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ypel4
• Phenotype: immune system phenotype; hematopoietic system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Cellular component: nucleolus
• Molecular function: metal ion binding