SREBF2
Basic information
Region (hg38): 22:41833078-41907307
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (52 variants)
- not provided (36 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SREBF2 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 | 8 | |||||
missense | 50 | 56 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region ? | 0 | |||||
non coding ? | 23 | 24 | ||||
Total | 0 | 0 | 50 | 4 | 34 |
Variants in SREBF2
This is a list of pathogenic ClinVar variants found in the SREBF2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
22-41833088-G-C | Benign (May 17, 2021) | |||
22-41833283-G-C | not specified | Uncertain significance (Oct 26, 2022) | ||
22-41833328-G-C | not specified | Uncertain significance (Jan 03, 2024) | ||
22-41866891-T-C | not specified | Uncertain significance (Jul 11, 2023) | ||
22-41866943-T-C | Benign (Dec 31, 2019) | |||
22-41867020-C-A | not specified | Uncertain significance (May 10, 2022) | ||
22-41867050-C-G | not specified | Uncertain significance (Nov 21, 2023) | ||
22-41867088-G-C | not specified | Uncertain significance (May 25, 2022) | ||
22-41867108-C-A | Benign (May 06, 2021) | |||
22-41867151-C-T | not specified | Uncertain significance (Apr 13, 2022) | ||
22-41867200-C-T | not specified | Uncertain significance (Aug 17, 2022) | ||
22-41867268-A-G | not specified | Uncertain significance (Jun 03, 2022) | ||
22-41868748-G-T | not specified | Uncertain significance (Oct 26, 2022) | ||
22-41868771-G-A | Benign (Dec 31, 2019) | |||
22-41868792-G-A | SREBF2-related disorder | Likely benign (May 07, 2019) | ||
22-41870958-C-G | not specified | Uncertain significance (Feb 27, 2023) | ||
22-41870965-T-C | not specified | Uncertain significance (Oct 06, 2022) | ||
22-41870979-A-C | not specified | Uncertain significance (Aug 13, 2021) | ||
22-41870994-G-A | not specified | Uncertain significance (Aug 17, 2022) | ||
22-41871192-C-T | Benign (May 17, 2021) | |||
22-41873624-C-T | Benign (May 15, 2021) | |||
22-41873846-A-G | not specified | Uncertain significance (Dec 04, 2023) | ||
22-41873847-T-C | not specified | Uncertain significance (Nov 29, 2021) | ||
22-41873934-A-G | not specified | Uncertain significance (Dec 20, 2023) | ||
22-41873984-G-A | not specified | Uncertain significance (Jul 27, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SREBF2 | protein_coding | protein_coding | ENST00000361204 | 19 | 74204 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.207 | 0.793 | 125720 | 0 | 28 | 125748 | 0.000111 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.679 | 605 | 654 | 0.925 | 0.0000427 | 7310 |
Missense in Polyphen | 180 | 225.29 | 0.79899 | 2486 | ||
Synonymous | -0.178 | 275 | 271 | 1.01 | 0.0000177 | 2405 |
Loss of Function | 5.05 | 12 | 50.9 | 0.236 | 0.00000280 | 531 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000331 | 0.000329 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.0000925 | 0.0000924 |
European (Non-Finnish) | 0.000133 | 0.000132 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.0000327 | 0.0000327 |
Other | 0.000357 | 0.000326 |
dbNSFP
Source:
- Function
- FUNCTION: Transcriptional activator required for lipid homeostasis. Regulates transcription of the LDL receptor gene as well as the cholesterol and to a lesser degree the fatty acid synthesis pathway (By similarity). Binds the sterol regulatory element 1 (SRE-1) (5'-ATCACCCCAC-3') found in the flanking region of the LDRL and HMG-CoA synthase genes. {ECO:0000250}.;
- Pathway
- Sterol Regulatory Element-Binding Proteins (SREBP) signalling;SREBF and miR33 in cholesterol and lipid homeostasis;Angiopoietin Like Protein 8 Regulatory Pathway;Metabolism of lipids;Regulation of cholesterol biosynthesis by SREBP (SREBF);Metabolism;Metabolism of steroids;srebp control of lipid synthesis;Activation of gene expression by SREBF (SREBP)
(Consensus)
Recessive Scores
- pRec
- 0.474
Intolerance Scores
- loftool
- 0.357
- rvis_EVS
- -1.83
- rvis_percentile_EVS
- 2.09
Haploinsufficiency Scores
- pHI
- 0.660
- hipred
- Y
- hipred_score
- 0.800
- ghis
- 0.555
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 1.00
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | High |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Srebf2
- Phenotype
- liver/biliary system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; homeostasis/metabolism phenotype;
Zebrafish Information Network
- Gene name
- srebf2
- Affected structure
- liver
- Phenotype tag
- abnormal
- Phenotype quality
- decreased size
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;lipid metabolic process;cholesterol metabolic process;cellular response to starvation;positive regulation of cholesterol storage;cholesterol homeostasis;regulation of cholesterol biosynthetic process;positive regulation of transcription by RNA polymerase II;cellular response to low-density lipoprotein particle stimulus;cellular response to laminar fluid shear stress;regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter;negative regulation of cholesterol efflux;positive regulation of pri-miRNA transcription by RNA polymerase II;regulation of autophagy of mitochondrion;positive regulation of protein targeting to mitochondrion
- Cellular component
- Golgi membrane;nucleus;nucleoplasm;cytoplasm;mitochondrion;endoplasmic reticulum;endoplasmic reticulum membrane;cytosol;ER to Golgi transport vesicle membrane;SREBP-SCAP-Insig complex;intracellular membrane-bounded organelle
- Molecular function
- C-8 sterol isomerase activity;RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;protein binding;protein C-terminus binding;protein dimerization activity;E-box binding