YIPF6
Basic information
Region (hg38): X:68498562-68537282
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the YIPF6 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 | 13 | 15 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 13 | 1 | 1 |
Variants in YIPF6
This is a list of pathogenic ClinVar variants found in the YIPF6 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| X-68511916-T-C | not specified | Uncertain significance (Jun 23, 2023) | ||
| X-68511918-A-G | not specified | Uncertain significance (May 16, 2022) | ||
| X-68511925-G-A | not specified | Uncertain significance (Jun 11, 2021) | ||
| X-68511930-C-T | not specified | Uncertain significance (Sep 02, 2024) | ||
| X-68511931-G-A | not specified | Uncertain significance (Nov 13, 2024) | ||
| X-68511956-T-A | not specified | Uncertain significance (Apr 07, 2023) | ||
| X-68513402-G-A | not specified | Uncertain significance (Aug 05, 2024) | ||
| X-68513403-A-T | not specified | Uncertain significance (Sep 29, 2023) | ||
| X-68518790-A-G | not specified | Uncertain significance (Jan 31, 2025) | ||
| X-68521385-G-C | Benign (May 08, 2018) | |||
| X-68521395-A-T | not specified | Uncertain significance (Dec 10, 2024) | ||
| X-68521420-A-C | not specified | Uncertain significance (Sep 01, 2021) | ||
| X-68521431-T-G | not specified | Uncertain significance (Jan 07, 2025) | ||
| X-68522824-A-G | not specified | Likely benign (Dec 30, 2023) | ||
| X-68522851-C-A | not specified | Uncertain significance (Jan 03, 2024) | ||
| X-68522866-T-C | not specified | Uncertain significance (Nov 09, 2021) | ||
| X-68531925-G-A | not specified | Uncertain significance (Jan 17, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| YIPF6 | protein_coding | protein_coding | ENST00000462683 | 7 | 38963 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.897 | 0.102 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.21 | 55 | 86.8 | 0.634 | 0.00000660 | 1528 |
| Missense in Polyphen | 17 | 34.984 | 0.48593 | 648 | ||
| Synonymous | 0.716 | 23 | 27.8 | 0.827 | 0.00000189 | 477 |
| Loss of Function | 2.52 | 0 | 7.37 | 0.00 | 5.45e-7 | 133 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: May be required for stable YIPF1 and YIPF2 protein expression. {ECO:0000269|PubMed:28286305}.;
- Pathway
- Golgi Associated Vesicle Biogenesis;Clathrin derived vesicle budding;trans-Golgi Network Vesicle Budding;Vesicle-mediated transport;Membrane Trafficking
(Consensus)
Recessive Scores
- pRec
- 0.0654
Intolerance Scores
- loftool
- 0.471
- rvis_EVS
- -0.05
- rvis_percentile_EVS
- 49.39
Haploinsufficiency Scores
- pHI
- 0.151
- hipred
- N
- hipred_score
- 0.390
- ghis
- 0.585
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.903
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Yipf6
- Phenotype
- mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); immune system phenotype; digestive/alimentary phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- intestinal epithelial cell development
- Cellular component
- Golgi trans cisterna;Golgi membrane;endoplasmic reticulum;Golgi medial cisterna;cis-Golgi network;trans-Golgi network;integral component of membrane;COPII-coated ER to Golgi transport vesicle
- Molecular function
- protein binding;identical protein binding