YIPF2

Yip1 domain family member 2, the group of Yip1 domain containing

Basic information

Region (hg38): 19:10922185-10928681

Links

ENSG00000130733 ∙ NCBI:78992 ∙ OMIM:617522 ∙ HGNC:28476 ∙ Uniprot:Q9BWQ6 ∙ 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 YIPF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the YIPF2 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				1		1
missense			41	5		46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	41	6	0

Variants in YIPF2

This is a list of pathogenic ClinVar variants found in the YIPF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-10923313-G-A		not specified	Uncertain significance (Nov 27, 2023)
19-10923319-G-C		not specified	Uncertain significance (Apr 08, 2024)
19-10923331-G-A		not specified	Uncertain significance (Dec 15, 2023)
19-10923356-T-C		not specified	Uncertain significance (Oct 03, 2024)
19-10923358-T-C		not specified	Uncertain significance (Sep 12, 2023)
19-10923361-G-A		not specified	Uncertain significance (Dec 09, 2024)
19-10923374-C-T		not specified	Uncertain significance (Apr 01, 2024)
19-10923375-G-T		not specified	Likely benign (Dec 13, 2022)
19-10923382-G-A		not specified	Likely benign (Dec 14, 2023)
19-10923391-G-A		not specified	Uncertain significance (Oct 08, 2024)
19-10923400-A-T		not specified	Uncertain significance (Sep 25, 2023)
19-10923405-C-G		not specified	Likely benign (Jul 09, 2021)
19-10923530-C-T		not specified	Uncertain significance (May 08, 2024)
19-10923533-C-A		not specified	Uncertain significance (Jul 20, 2021)
19-10923561-C-G		not specified	Uncertain significance (Aug 11, 2024)
19-10923563-T-G			Likely benign (Mar 01, 2022)
19-10923566-T-C		not specified	Uncertain significance (Nov 21, 2023)
19-10923596-A-G		not specified	Uncertain significance (Jun 10, 2024)
19-10923605-C-T		not specified	Uncertain significance (Aug 09, 2021)
19-10923661-G-A		not specified	Uncertain significance (Aug 04, 2024)
19-10923664-A-G		not specified	Uncertain significance (Feb 11, 2025)
19-10923673-A-G		not specified	Uncertain significance (Mar 02, 2023)
19-10923877-C-T		not specified	Uncertain significance (Jul 17, 2024)
19-10923910-C-T		not specified	Uncertain significance (Jul 16, 2024)
19-10923916-C-T		not specified	Uncertain significance (Oct 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
YIPF2	protein_coding	protein_coding	ENST00000586748	8	5914

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.32e-8	0.375	125623	0	107	125730	0.000426

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.142	197	191	1.03	0.0000121	1996
Missense in Polyphen		70	69.239	1.011		802
Synonymous	0.418	85	90.0	0.944	0.00000601	679
Loss of Function	0.727	13	16.2	0.805	6.91e-7	179

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000940	0.000937
Ashkenazi Jewish	0.0000996	0.0000992
East Asian	0.000218	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000487	0.000475
Middle Eastern	0.000218	0.000217
South Asian	0.000426	0.000425
Other	0.000825	0.000815

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.103

Intolerance Scores

• loftool: 0.383
• rvis_EVS: -0.2
• rvis_percentile_EVS: 38.98

Haploinsufficiency Scores

• pHI: 0.161
• hipred: N
• hipred_score: 0.170
• ghis: 0.517

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.908

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Yipf2

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