STARD4
Basic information
Region (hg38): 5:111496033-111512590
Links
Phenotypes
GenCC
Source:
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 STARD4 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 | 10 | 10 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 10 | 0 | 0 |
Variants in STARD4
This is a list of pathogenic ClinVar variants found in the STARD4 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-111499972-G-A | not specified | Uncertain significance (Oct 07, 2024) | ||
| 5-111499975-G-T | not specified | Uncertain significance (Dec 06, 2022) | ||
| 5-111500076-G-T | not specified | Uncertain significance (Nov 25, 2024) | ||
| 5-111500085-T-C | not specified | Uncertain significance (Oct 28, 2023) | ||
| 5-111501062-G-A | not specified | Uncertain significance (Mar 06, 2023) | ||
| 5-111501073-T-C | not specified | Uncertain significance (Jul 17, 2024) | ||
| 5-111501100-C-T | not specified | Uncertain significance (Oct 20, 2023) | ||
| 5-111501981-A-G | not specified | Uncertain significance (Jan 31, 2023) | ||
| 5-111502017-C-T | not specified | Uncertain significance (Jul 09, 2024) | ||
| 5-111507424-G-C | not specified | Uncertain significance (Jun 28, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| STARD4 | protein_coding | protein_coding | ENST00000296632 | 5 | 16558 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 6.99e-11 | 0.0197 | 125650 | 0 | 95 | 125745 | 0.000378 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.663 | 93 | 113 | 0.824 | 0.00000587 | 1347 |
| Missense in 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 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000460 | 0.000460 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.000141 | 0.000139 |
| European (Non-Finnish) | 0.000529 | 0.000510 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000528 | 0.000523 |
| Other | 0.000699 | 0.000652 |
dbNSFP
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}.;
- Pathway
- Metabolism of lipids;Metabolism;Pregnenolone biosynthesis;Metabolism of steroid hormones;Metabolism of steroids;Steroid hormones
(Consensus)
Recessive Scores
- pRec
- 0.122
Intolerance Scores
- loftool
- 0.694
- rvis_EVS
- -0.3
- rvis_percentile_EVS
- 32.62
Haploinsufficiency Scores
- pHI
- 0.129
- hipred
- N
- hipred_score
- 0.350
- ghis
- 0.626
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.616
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Stard4
- Phenotype
- liver/biliary system phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype;
Gene ontology
- 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
- Cellular component
- cytoplasmic vesicle
- Molecular function
- cholesterol binding;cholesterol transporter activity