YIPF4

Yip1 domain family member 4, the group of Yip1 domain containing

Basic information

Region (hg38): 2:32277903-32316594

Links

ENSG00000119820 ∙ NCBI:84272 ∙ OMIM:617534 ∙ HGNC:28145 ∙ Uniprot:Q9BSR8 ∙ 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 YIPF4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the YIPF4 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			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in YIPF4

This is a list of pathogenic ClinVar variants found in the YIPF4 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-32278169-G-T		not specified	Uncertain significance (May 18, 2023)
2-32278183-T-G		not specified	Uncertain significance (May 15, 2024)
2-32290516-A-C		not specified	Uncertain significance (Mar 14, 2023)
2-32292197-T-A		not specified	Uncertain significance (Jul 22, 2022)
2-32292240-G-A		not specified	Uncertain significance (Jan 24, 2024)
2-32292264-A-C		not specified	Uncertain significance (Sep 17, 2021)
2-32292307-G-T		not specified	Uncertain significance (Jun 27, 2022)
2-32292322-A-G		not specified	Uncertain significance (Aug 15, 2023)
2-32292332-T-C		not specified	Uncertain significance (Dec 19, 2023)
2-32292335-A-G		not specified	Uncertain significance (Aug 23, 2021)
2-32298286-T-C		not specified	Uncertain significance (Aug 02, 2021)
2-32298288-C-A		not specified	Uncertain significance (Jan 04, 2022)
2-32301397-G-A		not specified	Uncertain significance (Mar 01, 2023)
2-32301478-G-A		not specified	Uncertain significance (Nov 08, 2022)
2-32305501-T-C		not specified	Uncertain significance (Sep 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
YIPF4	protein_coding	protein_coding	ENST00000238831	6	38685

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0608	0.924	125711	0	6	125717	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.336	105	115	0.912	0.00000499	1527
Missense in Polyphen		22	33.539	0.65595		446
Synonymous	0.171	42	43.4	0.967	0.00000199	494
Loss of Function	2.12	4	11.9	0.336	5.79e-7	163

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000180	0.0000176
Middle Eastern	0.000109	0.000109
South Asian	0.0000332	0.0000327
Other	0.000173	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in the maintenance of the Golgi structure. {ECO:0000269|PubMed:21757827}.

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.323
• rvis_EVS: 0.37
• rvis_percentile_EVS: 74.95

Haploinsufficiency Scores

• pHI: 0.254
• hipred: Y
• hipred_score: 0.517
• ghis: 0.454

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.925

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Yipf4

Gene ontology

• Cellular component: endoplasmic reticulum;Golgi apparatus;plasma membrane;integral component of membrane;intracellular membrane-bounded organelle
• Molecular function: protein binding