YIPF6
protein-codingYip1 domain family member 6, the group of Yip1 domain containing
Gene summary
Predicted to enable identical protein binding activity. Predicted to be involved in endoplasmic reticulum to Golgi vesicle-mediated transport. Predicted to act upstream of or within intestinal epithelial cell development. Located in Golgi apparatus and endoplasmic reticulum. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~38.7 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to YIPF6 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_173834.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 6 | 6 | ||||
| missense | 45 | 1 | 1 | 47 | ||
| nonsense | 2 | 2 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 13 | 13 | ||||
| Total | 0 | 0 | 66 | 1 | 1 | 68 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_776195.2 | 7 | MANE Select | |
| Ensembl | ENSP00000417573.1 | 7 | MANE Select | |
| RefSeq | NP_001182143.1 | 6 | Standard | |
| Ensembl | ENSP00000363751.2 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Golgi Associated Vesicle Biogenesis
- Clathrin derived vesicle budding
- trans-Golgi Network Vesicle Budding
- Vesicle-mediated transport
- Membrane Trafficking
Biological Process
- intestinal epithelial cell development
Molecular Function
- protein binding
- identical protein binding
Cellular Component
- Golgi trans cisterna
- Golgi membrane
- endoplasmic reticulum
- Golgi medial cisterna
- cis-Golgi network
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000462683
- Coding exons
- 7
- Length
- 38963
- Individuals with no LoFs
- 0
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 0
- Defined
- 0
- p
- 0.00
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.21 | 55 | 86.8 | 0.634 | 0.00000660 | 1528 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May be required for stable YIPF1 and YIPF2 protein expression. {ECO:0000269|PubMed:28286305}.;
Recessive Scores
- pRec
- 0.0654
Intolerance Scores
- LoFtool
- 0.471
- RVIS EVS
- -0.05
- RVIS percentile EVS
- 49.39
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.903
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |