MVB12A
protein-codingmultivesicular body subunit 12A, the group of ESCRT-I
Gene summary
Enables lipid binding activity and ubiquitin binding activity. Involved in regulation of epidermal growth factor receptor signaling pathway. Located in centrosome; cytosol; and vesicle. Part of ESCRT I complex. [provided by Alliance of Genome Resources, Jun 2026]
- FAM125A
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~28.0 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 MVB12A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_138401.4. 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 | 0 | |||||
| missense | 48 | 4 | 52 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 50 | 4 | 0 | 54 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_612410.1 | 9 | MANE Select | |
| Ensembl | ENSP00000324810.6 | 9 | MANE Select | |
| RefSeq | NP_001291476.1 | 7 | Standard | |
| Ensembl | ENSP00000433677.1 | 7 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Endocytosis - Homo sapiens (human)
- Disease
- Vesicle-mediated transport
- Membrane Trafficking
- Assembly Of The HIV Virion
Biological Process
- protein transport
- endosomal transport
- macroautophagy
- viral life cycle
- virus maturation
Molecular Function
- protein binding
- lipid binding
- SH3 domain binding
- ubiquitin binding
Cellular Component
- ESCRT I complex
- nucleoplasm
- Golgi apparatus
- centrosome
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000317040
- Coding exons
- 9
- Length
- 28003
- Individuals with no LoFs
- 125709
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 38
- Defined
- 125747
- p
- 0.000151
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.202 | 167 | 160 | 1.04 | 0.00000878 | 1724 |
| Missense (PolyPhen) | 64 | 60.383 | 1.0599 | 675 | ||
| Synonymous | 0.921 | 59 | 68.7 | 0.859 | 0.00000376 | 584 |
| Loss of Function | 1.19 | 10 | 15.0 | 0.667 | 8.84e-7 | 155 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.00026 | 0.00026 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00022 | 0.00022 | rare |
| Finnish | 0.000049 | 0.000046 | rare |
| European (Non-Finnish) | 0.00012 | 0.00012 | rare |
| South Asian | 0.00033 | 0.00033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Component of the ESCRT-I complex, a regulator of vesicular trafficking process. Required for the sorting of endocytic ubiquitinated cargos into multivesicular bodies. May be involved in the ligand-mediated internalization and down- regulation of EGF receptor. {ECO:0000269|PubMed:16895919}.;
Intolerance Scores
- RVIS EVS
- 0.35
- RVIS percentile EVS
- 74.37
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |