PRELID3B
protein-codingPRELI domain containing 3B, the group of PRELI domain containing
Gene summary
Predicted to enable phosphatidic acid transfer activity. Predicted to be involved in phospholipid transport. Located in mitochondrion. [provided by Alliance of Genome Resources, Jul 2025]
- C20orf45
- SLMO2
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~9.7 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 PRELID3B variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_016045.3. 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 | 26 | 26 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 27 | 0 | 0 | 27 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_057129.2 | 6 | MANE Select | |
| Ensembl | ENSP00000348206.4 | 6 | MANE Select | |
| RefSeq | NP_001243332.1 | 5 | Standard | |
| Ensembl | ENSP00000360072.5 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- phospholipid transport
Molecular Function
- phosphatidic acid transporter activity
Cellular Component
- mitochondrial intermembrane space
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000355937
- Coding exons
- 6
- Length
- 9765
- Individuals with no LoFs
- 124768
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 26
- Defined
- 124794
- p
- 0.000104
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.792 | 81 | 104 | 0.781 | 0.00000493 | 1259 |
| Missense (PolyPhen) | 8 | 17.643 | 0.45343 | 226 | ||
| Synonymous | 0.530 | 31 | 35.0 | 0.886 | 0.00000191 | 370 |
| Loss of Function | 2.03 | 3 | 9.89 | 0.303 | 4.99e-7 | 123 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000075 | 0.000065 | rare |
| Latino/Admixed American | 0.00021 | 0.00020 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.00048 | 0.00046 | rare |
| European (Non-Finnish) | 0.000036 | 0.000035 | rare |
| South Asian | 0.000065 | 0.000065 | rare |
| Other | 0.00035 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
Intolerance Scores
- RVIS EVS
- 0.28
- RVIS percentile EVS
- 71.08
Essentials
- Essential (gene trap)
- E