TVP23B
protein-codingtrans-golgi network vesicle protein 23 homolog B
Gene summary
Predicted to be involved in protein secretion and vesicle-mediated transport. Located in Golgi apparatus. [provided by Alliance of Genome Resources, Jun 2026]
- FAM18B
- FAM18B1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~25.6 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 TVP23B variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_016078.6. 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 | 1 | 1 | ||||
| missense | 29 | 29 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 33 | 0 | 0 | 33 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_057162.4 | 7 | MANE Select | |
| Ensembl | ENSP00000305654.8 | 7 | MANE Select | |
| RefSeq | NP_001303848.1 | 5 | Standard | |
| RefSeq | NP_001303849.1 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- protein secretion
- vesicle-mediated transport
Cellular Component
- integral component of Golgi membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000307767
- Coding exons
- 7
- Length
- 25720
- Individuals with no LoFs
- 125663
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 80
- Defined
- 125743
- p
- 0.000318
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.673 | 90 | 110 | 0.819 | 0.00000557 | 1349 |
| Missense (PolyPhen) | 12 | 21.251 | 0.56469 | 299 | ||
| Synonymous | -0.108 | 40 | 39.1 | 1.02 | 0.00000210 | 370 |
| Loss of Function | 1.44 | 7 | 12.5 | 0.561 | 5.94e-7 | 146 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000066 | 0.000062 | rare |
| Latino/Admixed American | 0.00018 | 0.00017 | rare |
| Ashkenazi Jewish | 0.0033 | 0.0032 | notable |
| East Asian | 0.000059 | 0.000054 | rare |
| Finnish | 0.00066 | 0.00065 | rare |
| European (Non-Finnish) | 0.00017 | 0.00017 | rare |
| South Asian | 0.00013 | 0.00013 | rare |
| Other | 0.00054 | 0.00049 | rare |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.100
Intolerance Scores
- RVIS EVS
- 0.08
- RVIS percentile EVS
- 59.76
Essentials
- Essential (CRISPR)
- N
- Essential (gene trap)
- N
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Medium |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Medium | Medium |