SP3
Sp3 transcription factor, the group of Zinc fingers C2H2-type|Sp transcription factors
Basic information
Region (hg38): 2:173880850-173965373
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (95 variants)
- not_provided (3 variants)
- See_cases (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SP3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003111.5. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 3 | 4 | |||
| missense | 98 | 1 | 99 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 2 | 2 | ||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 104 | 1 | 3 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SP3 | protein_coding | protein_coding | ENST00000310015 | 7 | 59244 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 125729 | 0 | 2 | 125731 | 0.00000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.63 | 309 | 401 | 0.771 | 0.0000199 | 5033 |
| Missense in Polyphen | 80 | 145.7 | 0.54906 | 1900 | ||
| Synonymous | -2.82 | 192 | 148 | 1.29 | 0.00000781 | 1618 |
| Loss of Function | 5.11 | 1 | 32.4 | 0.0308 | 0.00000164 | 351 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000964 | 0.00000879 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcriptional factor that can act as an activator or repressor depending on isoform and/or post-translational modifications. Binds to GT and GC boxes promoter elements. Competes with SP1 for the GC-box promoters. Weak activator of transcription but can activate a number of genes involved in different processes such as cell-cycle regulation, hormone- induction and house-keeping. {ECO:0000269|PubMed:10391891, ECO:0000269|PubMed:11812829, ECO:0000269|PubMed:12419227, ECO:0000269|PubMed:12837748, ECO:0000269|PubMed:15247228, ECO:0000269|PubMed:15494207, ECO:0000269|PubMed:15554904, ECO:0000269|PubMed:16781829, ECO:0000269|PubMed:17548428, ECO:0000269|PubMed:18187045, ECO:0000269|PubMed:18617891, ECO:0000269|PubMed:9278495}.;
- Pathway
- Selenium Metabolism and Selenoproteins;MECP2 and Associated Rett Syndrome;Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways;overview of telomerase rna component gene hterc transcriptional regulation;effects of calcineurin in keratinocyte differentiation;SUMOylation of transcription factors;Post-translational protein modification;SUMO E3 ligases SUMOylate target proteins;Metabolism of proteins;SUMOylation;Regulation of Telomerase;Regulation of nuclear SMAD2/3 signaling
(Consensus)
Recessive Scores
- pRec
- 0.191
Intolerance Scores
- loftool
- 0.122
- rvis_EVS
- -0.07
- rvis_percentile_EVS
- 48.69
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.339
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;ossification;natural killer cell differentiation;trophectodermal cell differentiation;liver development;embryonic placenta development;regulation of transcription, DNA-templated;regulation of transcription by RNA polymerase II;B cell differentiation;T cell differentiation;megakaryocyte differentiation;monocyte differentiation;lung development;granulocyte differentiation;enucleate erythrocyte differentiation;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;embryonic camera-type eye morphogenesis;embryonic skeletal system development;embryonic process involved in female pregnancy;definitive hemopoiesis
- Cellular component
- nucleus;nucleoplasm;PML body;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;DNA-binding transcription repressor activity, RNA polymerase II-specific;chromatin binding;protein binding;metal ion binding