YIPF7

Yip1 domain family member 7, the group of Yip1 domain containing

Basic information

Region (hg38): 4:44622088-44678556

Links

ENSG00000177752 ∙ NCBI:285525 ∙ OMIM:619754 ∙ HGNC:26825 ∙ Uniprot:Q8N8F6 ∙ 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 YIPF7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the YIPF7 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			1			1
non coding			1			1
Total	0	0	23	0	0

Variants in YIPF7

This is a list of pathogenic ClinVar variants found in the YIPF7 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-44622466-G-C		not specified	Uncertain significance (Jul 05, 2023)
4-44622481-T-G		not specified	Uncertain significance (Aug 17, 2021)
4-44622484-C-T		not specified	Uncertain significance (Jul 16, 2024)
4-44622491-T-A		not specified	Uncertain significance (Apr 25, 2023)
4-44622553-G-A		not specified	Uncertain significance (May 07, 2024)
4-44624659-C-A		not specified	Uncertain significance (Nov 16, 2021)
4-44624665-C-T		not specified	Uncertain significance (Aug 09, 2021)
4-44624682-T-C		not specified	Uncertain significance (Jun 16, 2023)
4-44624692-C-T		not specified	Uncertain significance (Apr 06, 2022)
4-44624704-T-A		not specified	Uncertain significance (Dec 22, 2023)
4-44624725-T-C		not specified	Uncertain significance (Jul 27, 2024)
4-44624754-T-C		not specified	Uncertain significance (Nov 08, 2022)
4-44629409-C-G		not specified	Uncertain significance (May 01, 2024)
4-44629426-C-A		not specified	Uncertain significance (Aug 09, 2021)
4-44629468-T-C		not specified	Uncertain significance (Feb 05, 2024)
4-44629508-C-A		not specified	Uncertain significance (Aug 16, 2022)
4-44635958-T-A		not specified	Uncertain significance (Aug 13, 2021)
4-44635963-G-A		not specified	Uncertain significance (Oct 29, 2024)
4-44635988-T-C		not specified	Uncertain significance (Oct 09, 2024)
4-44636023-G-A		not specified	Uncertain significance (Jun 17, 2024)
4-44636071-T-C		not specified	Uncertain significance (Nov 28, 2024)
4-44650012-G-T		not specified	Uncertain significance (Aug 13, 2021)
4-44650100-T-A		not specified	Uncertain significance (Jan 31, 2024)
4-44651599-G-T		not specified	Uncertain significance (Jan 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
YIPF7	protein_coding	protein_coding	ENST00000332990	6	56488

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000818	0.531	124390	2	188	124580	0.000763

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.401	141	128	1.10	0.00000584	1793
Missense in Polyphen		55	49.321	1.1151		696
Synonymous	-1.44	60	47.4	1.27	0.00000250	522
Loss of Function	0.709	9	11.6	0.775	4.93e-7	161

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00989	0.00979
Ashkenazi Jewish	0.00	0.00
East Asian	0.000557	0.000557
Finnish	0.00	0.00
European (Non-Finnish)	0.0000465	0.0000443
Middle Eastern	0.000557	0.000557
South Asian	0.000200	0.000196
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.537
• rvis_EVS: -0.12
• rvis_percentile_EVS: 45.13

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.187
• ghis: 0.491

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0326

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Yipf7

Gene ontology

• Cellular component: endoplasmic reticulum membrane;Golgi apparatus;integral component of membrane