PRELID1
PRELI domain containing 1, the group of PRELI domain containing
Basic information
Region (hg38): 5:177303799-177306949
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PRELID1 gene is commonly pathogenic or not.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 8 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 8 | 0 | 0 |
Variants in PRELID1
This is a list of pathogenic ClinVar variants found in the PRELID1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-177304019-C-T | not specified | Uncertain significance (Apr 20, 2023) | ||
| 5-177304031-G-T | not specified | Uncertain significance (Nov 03, 2023) | ||
| 5-177304647-A-T | not specified | Uncertain significance (Feb 23, 2023) | ||
| 5-177306140-A-G | not specified | Uncertain significance (Dec 27, 2023) | ||
| 5-177306521-C-T | not specified | Uncertain significance (Mar 02, 2023) | ||
| 5-177306541-A-C | not specified | Likely benign (Nov 13, 2024) | ||
| 5-177306544-C-A | not specified | Uncertain significance (Jan 07, 2022) | ||
| 5-177306561-G-T | not specified | Uncertain significance (Jun 27, 2023) | ||
| 5-177306563-T-G | not specified | Uncertain significance (Jan 26, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PRELID1 | protein_coding | protein_coding | ENST00000303204 | 5 | 3186 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.115 | 0.880 | 125734 | 0 | 13 | 125747 | 0.0000517 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.26 | 88 | 128 | 0.687 | 0.00000728 | 1419 |
| Missense in Polyphen | 16 | 29.785 | 0.53719 | 402 | ||
| Synonymous | 1.10 | 41 | 51.0 | 0.804 | 0.00000287 | 429 |
| Loss of Function | 2.44 | 4 | 13.8 | 0.291 | 9.00e-7 | 122 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000246 | 0.000246 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000528 | 0.0000527 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.0000654 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in the modulation of the mitochondrial apoptotic pathway by ensuring the accumulation of cardiolipin (CL) in mitochondrial membranes. In vitro, the TRIAP1:PRELID1 complex mediates the transfer of phosphatidic acid (PA) between liposomes and probably functions as a PA transporter across the mitochondrion intermembrane space to provide PA for CL synthesis in the inner membrane. Regulates the mitochondrial apoptotic pathway in primary Th cells. Regulates Th cell differentiation by down-regulating STAT6 thereby reducing IL-4-induced Th2 cell number. May be important for the development of vital and immunocompetent organs. {ECO:0000269|PubMed:18945965, ECO:0000269|PubMed:21364629, ECO:0000269|PubMed:23931759}.;
- Pathway
- 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;Transcriptional Regulation by TP53
(Consensus)
Recessive Scores
- pRec
- 0.111
Intolerance Scores
- loftool
- rvis_EVS
- -0.16
- rvis_percentile_EVS
- 41.25
Haploinsufficiency Scores
- pHI
- 0.326
- hipred
- Y
- hipred_score
- 0.673
- ghis
- 0.625
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.262
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Low | Medium |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Prelid1
- Phenotype
- normal phenotype;
Gene ontology
- Biological process
- apoptotic process;immune response;multicellular organism development;negative regulation of mitochondrial membrane potential;positive regulation of endopeptidase activity;phospholipid transport;regulation of apoptotic process;negative regulation of apoptotic process;regulation of T cell differentiation;regulation of mitochondrial membrane potential;positive regulation of T cell apoptotic process;negative regulation of release of cytochrome c from mitochondria;regulation of membrane lipid distribution;positive regulation of cellular respiration;positive regulation of phospholipid transport
- Cellular component
- nucleoplasm;mitochondrion;mitochondrial intermembrane space;protein-containing complex
- Molecular function
- protein binding;phosphatidic acid transporter activity