UBAP1
protein-codingubiquitin associated protein 1, the group of ESCRT-I
Gene summary
This gene is a member of the UBA domain family, whose members include proteins having connections to ubiquitin and the ubiquitination pathway. The ubiquitin associated domain is thought to be a non-covalent ubiquitin binding domain consisting of a compact three helix bundle. This particular protein originates from a gene locus in a refined region on chromosome 9 undergoing loss of heterozygosity in nasopharyngeal carcinoma (NPC). Taking into account its cytogenetic location, this UBA domain family member is being studies as a putative target for mutation in nasopharyngeal carcinomas. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2010]
- UBAP
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~73.5 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0011489
Submitter: Orphanet
Inheritance Pattern: Unknown
Disease ID:MONDO:0007661
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0032737
Submitter: Illumina
Inheritance Pattern: AD
Disease ID:MONDO:0032737
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0032737
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0032737
Submitter: Labcorp Genetics (formerly Invitae)
Clinical Genomic Database (CGD)
Manifestation: Neurologic
Intervention: General
Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to UBAP1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_016525.5. 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 | 3 | 3 | ||||
| missense | 1 | 59 | 8 | 2 | 70 | |
| nonsense | 4 | 2 | 6 | |||
| start loss | 0 | |||||
| frameshift | 9 | 3 | 2 | 14 | ||
| splice donor/acceptor (+/-2bp) | 4 | 4 | ||||
| Total | 13 | 6 | 65 | 11 | 2 | 97 |
Highest pathogenic variant AF is 0.000009294728
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_057609.2 | 6 | MANE Select | |
| Ensembl | ENSP00000297661.4 | 6 | MANE Select | |
| RefSeq | NP_001164672.1 | 6 | Standard | |
| RefSeq | NP_001164673.1 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Disease
- Vesicle-mediated transport
- Membrane Trafficking
- Assembly Of The HIV Virion
- Budding and maturation of HIV virion
Biological Process
- protein transport
- endosomal transport
- viral life cycle
- ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway
Molecular Function
- protein binding
- ubiquitin binding
Cellular Component
- ESCRT I complex
- cytoplasm
- Golgi apparatus
- cytosol
- plasma membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000545103
- Coding exons
- 6
- Length
- 73519
- Individuals with no LoFs
- 125743
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 2
- Defined
- 125745
- p
- 0.00000795
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.869 | 240 | 281 | 0.854 | 0.0000142 | 3720 |
| Missense (PolyPhen) | 65 | 85.526 | 0.76 | 1236 | ||
| Synonymous | 0.111 | 107 | 108 | 0.986 | 0.00000584 | 1105 |
| Loss of Function | 3.32 | 2 | 16.6 | 0.120 | 6.98e-7 | 257 |
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 | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.0000088 | 0.0000088 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Component of the ESCRT-I complex, a regulator of vesicular trafficking process. Binds to ubiquitinated cargo proteins and is required for the sorting of endocytic ubiquitinated cargos into multivesicular bodies (MVBs). Plays a role in the proteasomal degradation of ubiquitinated cell-surface proteins, such as EGFR and BST2. {ECO:0000269|PubMed:21757351, ECO:0000269|PubMed:22405001}.;
Recessive Scores
- pRec
- 0.156
Intolerance Scores
- RVIS EVS
- -0.82
- RVIS percentile EVS
- 11.68
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- S
- Essential (gene trap)
- E
- Indispensability pred.
- N
- Indispensability score
- 0.00979
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |