YIPF1

Yip1 domain family member 1, the group of Yip1 domain containing

Basic information

Region (hg38): 1:53851718-53889798

Links

ENSG00000058799 ∙ NCBI:54432 ∙ OMIM:617521 ∙ HGNC:25231 ∙ Uniprot:Q9Y548 ∙ 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 YIPF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the YIPF1 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			22			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	0	0

Variants in YIPF1

This is a list of pathogenic ClinVar variants found in the YIPF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-53860113-G-A		not specified	Uncertain significance (May 03, 2023)
1-53860153-C-G		not specified	Uncertain significance (Jul 20, 2021)
1-53866205-A-G		not specified	Uncertain significance (May 04, 2022)
1-53866264-C-T		not specified	Uncertain significance (Oct 02, 2023)
1-53866280-G-A		not specified	Uncertain significance (Dec 19, 2022)
1-53866300-A-G		not specified	Uncertain significance (Oct 06, 2021)
1-53866364-G-C		not specified	Uncertain significance (Jun 29, 2023)
1-53866810-A-G		not specified	Uncertain significance (Jul 25, 2023)
1-53871383-T-C		not specified	Uncertain significance (Nov 09, 2023)
1-53871401-G-A		not specified	Uncertain significance (Jan 23, 2024)
1-53871408-C-T		not specified	Uncertain significance (May 16, 2023)
1-53871414-G-C		not specified	Uncertain significance (Dec 19, 2023)
1-53871467-G-A		not specified	Uncertain significance (Dec 19, 2023)
1-53878336-G-A		not specified	Uncertain significance (Dec 28, 2023)
1-53878362-C-G		not specified	Uncertain significance (Mar 07, 2023)
1-53878655-A-G		not specified	Uncertain significance (Jan 05, 2022)
1-53878694-G-C		not specified	Uncertain significance (Aug 17, 2021)
1-53883154-C-T		not specified	Uncertain significance (Jun 07, 2024)
1-53883158-T-G		not specified	Uncertain significance (Dec 01, 2022)
1-53883184-C-G		not specified	Uncertain significance (Sep 09, 2021)
1-53883208-C-G		not specified	Uncertain significance (Aug 14, 2023)
1-53883241-G-T		not specified	Uncertain significance (Nov 18, 2023)
1-53883259-T-C		not specified	Uncertain significance (Jul 11, 2023)
1-53883274-A-C		not specified	Uncertain significance (Jun 10, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
YIPF1	protein_coding	protein_coding	ENST00000072644	8	39016

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00318	0.987	124927	8	812	125747	0.00327

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.144	173	168	1.03	0.00000856	1988
Missense in Polyphen		56	68.997	0.81163		807
Synonymous	1.45	46	60.4	0.762	0.00000317	602
Loss of Function	2.26	7	17.1	0.410	8.93e-7	196

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00113	0.00113
Ashkenazi Jewish	0.0150	0.0150
East Asian	0.000164	0.000163
Finnish	0.00679	0.00667
European (Non-Finnish)	0.00315	0.00313
Middle Eastern	0.000164	0.000163
South Asian	0.00391	0.00380
Other	0.00327	0.00326

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.462
• rvis_EVS: -0.23
• rvis_percentile_EVS: 37.32

Haploinsufficiency Scores

• pHI: 0.166
• hipred: N
• hipred_score: 0.397
• ghis: 0.533

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.189

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Yipf1
• Phenotype: normal phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: vesicle-mediated transport
• Cellular component: Golgi trans cisterna;Golgi apparatus;Golgi medial cisterna;trans-Golgi network;integral component of membrane;transport vesicle;late endosome membrane
• Molecular function: protein binding;Rab GTPase binding