STARD4
protein-codingStAR related lipid transfer domain containing 4, the group of StAR related lipid transfer domain containing
Gene summary
Cholesterol homeostasis is regulated, at least in part, by sterol regulatory element (SRE)-binding proteins (e.g., SREBP1; MIM 184756) and by liver X receptors (e.g., LXRA; MIM 602423). Upon sterol depletion, LXRs are inactive and SREBPs are cleaved, after which they bind promoter SREs and activate genes involved in cholesterol biosynthesis and uptake. Sterol transport is mediated by vesicles or by soluble protein carriers, such as steroidogenic acute regulatory protein (STAR; MIM 600617). STAR is homologous to a family of proteins containing a 200- to 210-amino acid STAR-related lipid transfer (START) domain, including STARD4 (Soccio et al., 2002 [PubMed 12011452]).[supplied by OMIM, Mar 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~16.6 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 STARD4 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_139164.3. 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 | 23 | 23 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 23 | 0 | 0 | 23 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_631903.1 | 5 | MANE Select | |
| Ensembl | ENSP00000296632.3 | 5 | MANE Select | |
| RefSeq | NP_001294985.1 | 5 | Standard | |
| RefSeq | NP_001294986.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Metabolism of lipids
- Metabolism
- Pregnenolone biosynthesis
- Metabolism of steroid hormones
- Metabolism of steroids
Biological Process
- positive regulation of cholesterol esterification
- cholesterol transport involved in cholesterol storage
- intracellular cholesterol transport
- cholesterol import
- positive regulation of bile acid biosynthetic process
Molecular Function
- cholesterol binding
- cholesterol transporter activity
Cellular Component
- cytoplasmic vesicle
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000296632
- Coding exons
- 5
- Length
- 16558
- Individuals with no LoFs
- 125650
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 95
- Defined
- 125745
- p
- 0.000378
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.663 | 93 | 113 | 0.824 | 0.00000587 | 1347 |
| Missense (PolyPhen) | 32 | 36.492 | 0.8769 | 480 | ||
| Synonymous | 0.189 | 33 | 34.4 | 0.959 | 0.00000155 | 371 |
| Loss of Function | -0.756 | 14 | 11.3 | 1.24 | 6.26e-7 | 129 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.00040 | 0.00038 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.00014 | 0.00014 | rare |
| European (Non-Finnish) | 0.00053 | 0.00051 | rare |
| South Asian | 0.00053 | 0.00052 | rare |
| Other | 0.00070 | 0.00065 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May be involved in the intracellular transport of sterols or other lipids. May bind cholesterol or other sterols (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.122
Intolerance Scores
- LoFtool
- 0.694
- RVIS EVS
- -0.3
- RVIS percentile EVS
- 32.62
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.616
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |