SOX4
SRY-box transcription factor 4, the group of SRY-box transcription factors
Basic information
Region (hg38): 6:21593751-21598619
Links
Phenotypes
GenCC
Source:
- Coffin-Siris syndrome 10 (Strong), mode of inheritance: AD
- Coffin-Siris syndrome (Supportive), mode of inheritance: AD
- Coffin-Siris syndrome 10 (Moderate), mode of inheritance: AD
- Coffin-Siris syndrome 10 (Strong), mode of inheritance: AD
- atrial fibrillation (Limited), mode of inheritance: AD
- Coffin-Siris syndrome 10 (Strong), mode of inheritance: AD
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Intellectual developmental disorder with speech delay and dysmorphic facies (Coffin-Siris syndrome 10) | AD | Cardiovascular | The condition can involve congenital cardiac anomalies, and awareness may allow early management | Cardiovascular; Craniofacial; Musculoskeletal; Neurologic | 30661772 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_provided (108 variants)
- Inborn_genetic_diseases (87 variants)
- Coffin-Siris_syndrome_10 (41 variants)
- SOX4-related_disorder (21 variants)
- not_specified (6 variants)
- Intellectual_disability (5 variants)
- Developmental_delay (4 variants)
- Mild_facial_and_digital_morphological_abnormalities (4 variants)
- See_cases (2 variants)
- Neurodevelopmental_disorder (1 variants)
- Intellectual_disability,_mild (1 variants)
- SOX4-related_neurodevelopmental_disorder (1 variants)
- Disorder_of_sexual_differentiation (1 variants)
- Coffin-Siris_syndrome_1 (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SOX4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000003107.3. 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 | 27 | 32 | ||||
| missense | 13 | 148 | 10 | 173 | ||
| nonsense | 10 | |||||
| start loss | 0 | |||||
| frameshift | 10 | 15 | ||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 7 | 18 | 162 | 39 | 4 |
Highest pathogenic variant AF is 6.864492e-7
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SOX4 | protein_coding | protein_coding | ENST00000244745 | 1 | 4876 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.927 | 0.0731 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.17 | 150 | 196 | 0.765 | 0.00000902 | 2971 |
| Missense in Polyphen | 9 | 50.031 | 0.17989 | 563 | ||
| Synonymous | -5.14 | 157 | 93.7 | 1.67 | 0.00000469 | 1027 |
| Loss of Function | 2.68 | 0 | 8.34 | 0.00 | 3.61e-7 | 117 |
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) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcriptional activator that binds with high affinity to the T-cell enhancer motif 5'-AACAAAG-3' motif.;
- Pathway
- MicroRNAs in cancer - Homo sapiens (human);H19 action Rb-E2F1 signaling and CDK-β-catenin activity;Signaling by WNT;Signal Transduction;Deactivation of the beta-catenin transactivating complex;IL5;TCF dependent signaling in response to WNT
(Consensus)
Recessive Scores
- pRec
- 0.260
Haploinsufficiency Scores
- pHI
- 0.961
- hipred
- Y
- hipred_score
- 0.807
- ghis
- 0.471
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.903
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Sox4
- Phenotype
- digestive/alimentary phenotype; limbs/digits/tail phenotype; 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; immune system phenotype; renal/urinary system phenotype; skeleton phenotype; embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; 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); normal 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); endocrine/exocrine gland phenotype; craniofacial phenotype; homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region 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);
Zebrafish Information Network
- Gene name
- sox4b
- Affected structure
- glucagon secreting cell
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- skeletal system development;neural tube formation;pro-B cell differentiation;mitral valve morphogenesis;cardiac ventricle formation;cardiac right ventricle morphogenesis;atrial septum primum morphogenesis;noradrenergic neuron differentiation;regulation of transcription, DNA-templated;DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest;heart development;positive regulation of cell population proliferation;negative regulation of cell population proliferation;glial cell proliferation;spinal cord development;spinal cord motor neuron differentiation;glial cell development;cell differentiation;T cell differentiation;endocrine pancreas development;negative regulation of protein ubiquitination;regulation of protein stability;positive regulation of insulin secretion;somatic stem cell population maintenance;ascending aorta morphogenesis;glucose homeostasis;DNA damage response, detection of DNA damage;positive regulation of apoptotic process;positive regulation of translation;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;sympathetic nervous system development;protein stabilization;limb bud formation;ventricular septum morphogenesis;negative regulation of cell death;neuroepithelial cell differentiation;kidney morphogenesis;cellular response to glucose stimulus;positive regulation of canonical Wnt signaling pathway;positive regulation of N-terminal peptidyl-lysine acetylation
- Cellular component
- nucleus;nucleoplasm;cytoplasm;mitochondrion;nuclear transcription factor complex
- Molecular function
- transcription regulatory region sequence-specific DNA binding;RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;DNA-binding transcription factor activity;transcription coactivator activity;protein binding;protein heterodimerization activity