PRELID3A
protein-codingPRELI domain containing 3A, the group of PRELI domain containing
Gene summary
Enables phosphatidic acid transfer activity. Involved in phospholipid transport. Located in mitochondrion. [provided by Alliance of Genome Resources, Jul 2025]
- C18orf43
- SLMO1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~24.3 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 PRELID3A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001142405.2. 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 | 19 | 19 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 19 | 1 | 0 | 20 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001135877.1 | 6 | MANE Select | |
| Ensembl | ENSP00000404700.1 | 6 | MANE Select | |
| RefSeq | NP_001135878.1 | 5 | Standard | |
| RefSeq | NP_006544.2 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Gene expression (Transcription)
- Generic Transcription Pathway
- TP53 Regulates Transcription of Cell Death Genes
- RNA Polymerase II Transcription
- TP53 Regulates Transcription of Genes Involved in Cytochrome C Release
Biological Process
- phospholipid transport
Molecular Function
- protein binding
- phosphatidic acid transporter activity
Cellular Component
- mitochondrial intermembrane space
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000440960
- Coding exons
- 6
- Length
- 24343
- Individuals with no LoFs
- 125722
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 26
- Defined
- 125748
- p
- 0.000103
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.456 | 82 | 94.5 | 0.868 | 0.00000457 | 1111 |
| Missense (PolyPhen) | 36 | 42.914 | 0.83888 | 494 | ||
| Synonymous | -0.407 | 40 | 36.9 | 1.09 | 0.00000196 | 327 |
| Loss of Function | -0.769 | 12 | 9.45 | 1.27 | 4.87e-7 | 115 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0.00010 | 0.000099 | rare |
| East Asian | 0.00016 | 0.00016 | rare |
| Finnish | 0.000092 | 0.000092 | rare |
| European (Non-Finnish) | 0.00012 | 0.00011 | rare |
| South Asian | 0.00013 | 0.00013 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: In vitro, the TRIAP1:PRELID3A complex mediates the transfer of phosphatidic acid (PA) between liposomes and probably functions as a PA transporter across the mitochondrion intermembrane space. Phosphatidic acid import is required for cardiolipin (CL) synthesis in the mitochondrial inner membrane. {ECO:0000305|PubMed:26071602}.;
Recessive Scores
- pRec
- 0.108
Intolerance Scores
- RVIS EVS
- -0.19
- RVIS percentile EVS
- 39.68
Essentials
- Essential (gene trap)
- N