SP1
Sp1 transcription factor, the group of Zinc fingers C2H2-type|Sp transcription factors
Basic information
Region (hg38): 12:53380176-53416446
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 SP1 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 | 6 | |||||
| missense | 31 | 31 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 1 | |||||
| Total | 0 | 0 | 31 | 4 | 3 |
Variants in SP1
This is a list of pathogenic ClinVar variants found in the SP1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 12-53381649-A-G | Likely benign (Aug 02, 2018) | |||
| 12-53381725-A-G | not specified | Uncertain significance (Sep 20, 2023) | ||
| 12-53381734-A-C | not specified | Uncertain significance (Mar 19, 2024) | ||
| 12-53381795-C-G | not specified | Uncertain significance (Jun 17, 2024) | ||
| 12-53382190-C-G | Benign (Apr 24, 2018) | |||
| 12-53382192-A-G | not specified | Uncertain significance (Dec 14, 2023) | ||
| 12-53382215-A-G | not specified | Uncertain significance (Feb 01, 2023) | ||
| 12-53382216-C-T | not specified | Uncertain significance (Feb 12, 2024) | ||
| 12-53382245-C-T | not specified | Uncertain significance (Nov 18, 2022) | ||
| 12-53382308-A-G | not specified | Uncertain significance (Jun 18, 2021) | ||
| 12-53382323-A-G | not specified | Uncertain significance (Aug 10, 2023) | ||
| 12-53382330-C-T | not specified | Uncertain significance (Apr 23, 2024) | ||
| 12-53382387-A-G | not specified | Uncertain significance (Dec 14, 2023) | ||
| 12-53382459-T-C | not specified | Uncertain significance (Jul 05, 2023) | ||
| 12-53382572-G-C | not specified | Uncertain significance (Jul 25, 2023) | ||
| 12-53382627-C-G | not specified | Uncertain significance (Dec 16, 2022) | ||
| 12-53382629-A-G | not specified | Uncertain significance (May 07, 2024) | ||
| 12-53382770-G-C | not specified | Uncertain significance (Apr 20, 2023) | ||
| 12-53382840-C-G | not specified | Uncertain significance (Jul 12, 2023) | ||
| 12-53382878-G-T | not specified | Uncertain significance (Dec 03, 2024) | ||
| 12-53382889-A-T | not specified | Uncertain significance (Jul 13, 2022) | ||
| 12-53382904-C-G | Likely benign (May 20, 2018) | |||
| 12-53382915-A-G | not specified | Uncertain significance (Aug 01, 2022) | ||
| 12-53382924-G-C | not specified | Uncertain significance (Jun 30, 2022) | ||
| 12-53382938-A-G | not specified | Uncertain significance (Feb 06, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SP1 | protein_coding | protein_coding | ENST00000327443 | 6 | 36271 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.0000253 | 125725 | 0 | 1 | 125726 | 0.00000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.14 | 359 | 425 | 0.845 | 0.0000217 | 5106 |
| Missense in Polyphen | 48 | 56.116 | 0.85538 | 578 | ||
| Synonymous | -1.53 | 186 | 161 | 1.15 | 0.00000806 | 1665 |
| Loss of Function | 5.06 | 0 | 29.9 | 0.00 | 0.00000144 | 310 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000879 | 0.00000879 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcription factor that can activate or repress transcription in response to physiological and pathological stimuli. Binds with high affinity to GC-rich motifs and regulates the expression of a large number of genes involved in a variety of processes such as cell growth, apoptosis, differentiation and immune responses. Highly regulated by post-translational modifications (phosphorylations, sumoylation, proteolytic cleavage, glycosylation and acetylation). Binds also the PDGFR- alpha G-box promoter. May have a role in modulating the cellular response to DNA damage. Implicated in chromatin remodeling. Plays an essential role in the regulation of FE65 gene expression. In complex with ATF7IP, maintains telomerase activity in cancer cells by inducing TERT and TERC gene expression. Isoform 3 is a stronger activator of transcription than isoform 1. Positively regulates the transcription of the core clock component ARNTL/BMAL1 (PubMed:10391891, PubMed:11371615, PubMed:11904305, PubMed:14593115, PubMed:16377629, PubMed:16478997, PubMed:16943418, PubMed:17049555, PubMed:18171990, PubMed:18199680, PubMed:18239466, PubMed:18513490, PubMed:18619531, PubMed:19193796, PubMed:20091743, PubMed:21798247). Plays a role in the recruitment of SMARCA4/BRG1 on the c-FOS promoter. Plays a role in protecting cells against oxidative stress following brain injury by regulating the expression of RNF112 (By similarity). {ECO:0000250|UniProtKB:O89090, ECO:0000250|UniProtKB:Q01714, ECO:0000269|PubMed:10391891, ECO:0000269|PubMed:11371615, ECO:0000269|PubMed:11904305, ECO:0000269|PubMed:14593115, ECO:0000269|PubMed:16377629, ECO:0000269|PubMed:16478997, ECO:0000269|PubMed:16943418, ECO:0000269|PubMed:17049555, ECO:0000269|PubMed:18171990, ECO:0000269|PubMed:18199680, ECO:0000269|PubMed:18239466, ECO:0000269|PubMed:18513490, ECO:0000269|PubMed:18619531, ECO:0000269|PubMed:19193796, ECO:0000269|PubMed:20091743, ECO:0000269|PubMed:21798247}.;
- Pathway
- Cortisol synthesis and secretion - Homo sapiens (human);TGF-beta signaling pathway - Homo sapiens (human);Choline metabolism in cancer - Homo sapiens (human);Cushing,s syndrome - Homo sapiens (human);Breast cancer - Homo sapiens (human);Huntington,s disease - Homo sapiens (human);Mitophagy - animal - Homo sapiens (human);Estrogen signaling pathway - Homo sapiens (human);Pathways in cancer - Homo sapiens (human);Transcriptional misregulation in cancer - Homo sapiens (human);EGFR Inhibitor Pathway, Pharmacodynamics;Androgen receptor signaling pathway;Sterol Regulatory Element-Binding Proteins (SREBP) signalling;Integrated Breast Cancer Pathway;Leptin signaling pathway;IL17 signaling pathway;Androgen Receptor Network in Prostate Cancer;AGE-RAGE pathway;Corticotropin-releasing hormone signaling pathway;Adipogenesis;JAK-STAT;Constitutive Androstane Receptor Pathway;Estrogen Receptor Pathway;Nuclear Receptors Meta-Pathway;Myometrial Relaxation and Contraction Pathways;Copper homeostasis;Initiation of transcription and translation elongation at the HIV-1 LTR;MECP2 and Associated Rett Syndrome;TGF-beta Signaling Pathway;Mitochondrial Gene Expression;Liver steatosis AOP;Oxidative Stress;EGF-EGFR Signaling Pathway;Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways;Estrogen signaling pathway;Signal Transduction;Gene expression (Transcription);mechanism of gene regulation by peroxisome proliferators via ppara;human cytomegalovirus and map kinase pathways;overview of telomerase rna component gene hterc transcriptional regulation;effects of calcineurin in keratinocyte differentiation;overview of telomerase protein component gene htert transcriptional regulation;keratinocyte differentiation;mapkinase signaling pathway;Generic Transcription Pathway;Oncogene Induced Senescence;Metabolism of lipids;Cellular Senescence;Cellular responses to stress;RNA polymerase II transcribes snRNA genes;RNA Polymerase II Transcription;Regulation of cholesterol biosynthesis by SREBP (SREBF);HIF-2-alpha transcription factor network;Metabolism;p73 transcription factor network;SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription;Metabolism of steroids;AndrogenReceptor;Cellular responses to external stimuli;TGF_beta_Receptor;Transcriptional activity of SMAD2/SMAD3:SMAD4 heterotrimer;EGFR1;agrin in postsynaptic differentiation;Validated transcriptional targets of TAp63 isoforms;FOXA1 transcription factor network;Signaling by Nuclear Receptors;C-MYB transcription factor network;Gastrin;Direct p53 effectors;Leptin;Estrogen-dependent gene expression;Activation of gene expression by SREBF (SREBP);Signaling by TGF-beta Receptor Complex;Signaling by TGF-beta family members;ESR-mediated signaling;IL2 signaling events mediated by STAT5;Validated targets of C-MYC transcriptional repression;Regulation of Telomerase;AP-1 transcription factor network;HIF-1-alpha transcription factor network;FOXM1 transcription factor network;IL4-mediated signaling events;Validated transcriptional targets of AP1 family members Fra1 and Fra2;FOXA2 and FOXA3 transcription factor networks;Regulation of nuclear SMAD2/3 signaling;E2F transcription factor network
(Consensus)
Recessive Scores
- pRec
- 0.767
Intolerance Scores
- loftool
- rvis_EVS
- -0.93
- rvis_percentile_EVS
- 9.55
Haploinsufficiency Scores
- pHI
- 1.00
- hipred
- Y
- hipred_score
- 0.762
- ghis
- 0.661
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 1.00
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Sp1
- Phenotype
- craniofacial phenotype; homeostasis/metabolism 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); 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); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); growth/size/body region phenotype; vision/eye phenotype; limbs/digits/tail phenotype; skeleton phenotype; liver/biliary system phenotype; respiratory system phenotype; embryo phenotype;
Gene ontology
- Biological process
- regulation of transcription, DNA-templated;regulation of transcription by RNA polymerase II;positive regulation of gene expression;viral process;cellular response to insulin stimulus;response to hydroperoxide;snRNA transcription by RNA polymerase II;positive regulation of blood vessel endothelial cell migration;positive regulation by host of viral transcription;regulation of cholesterol biosynthetic process;positive regulation of angiogenesis;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;rhythmic process;regulation of phenotypic switching by transcription from RNA polymerase II promoter;positive regulation of hydrogen sulfide biosynthetic process;positive regulation of vascular endothelial cell proliferation
- Cellular component
- nuclear chromatin;nucleus;nucleoplasm;cytoplasm;transcriptional repressor complex;protein-DNA complex
- Molecular function
- RNA polymerase II regulatory region sequence-specific DNA binding;RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;proximal promoter sequence-specific DNA binding;RNA polymerase II repressing transcription factor binding;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA binding;double-stranded DNA binding;DNA-binding transcription factor activity;protein binding;protein C-terminus binding;transcription factor binding;histone acetyltransferase binding;protein homodimerization activity;histone deacetylase binding;bHLH transcription factor binding;sequence-specific DNA binding;transcription regulatory region DNA binding;metal ion binding;repressing transcription factor binding;HMG box domain binding