SOX8
Basic information
Region (hg38): 16:981444-986979
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (72 variants)
- not_provided (17 variants)
- SOX8-related_disorder (17 variants)
- 46,XY_disorder_of_sex_development (2 variants)
- Aplasia_of_the_ovary (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SOX8 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014587.5. 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 | 15 | 19 | ||||
| missense | 73 | 82 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 1 | 73 | 23 | 4 |
Highest pathogenic variant AF is 0.000028343207
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SOX8 | protein_coding | protein_coding | ENST00000293894 | 3 | 5172 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.672 | 0.327 | 122355 | 0 | 5 | 122360 | 0.0000204 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.888 | 230 | 271 | 0.848 | 0.0000192 | 2789 |
| Missense in Polyphen | 77 | 117.56 | 0.65499 | 1308 | ||
| Synonymous | -1.72 | 159 | 134 | 1.19 | 0.0000116 | 915 |
| Loss of Function | 2.72 | 2 | 12.3 | 0.163 | 6.07e-7 | 148 |
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 | 0.0000503 | 0.0000482 |
| European (Non-Finnish) | 0.0000291 | 0.0000273 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000346 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: May play a role in central nervous system, limb and facial development. May be involved in male sex determination. Binds the consensus motif 5'-[AT][AT]CAA[AT]G-3' (By similarity). {ECO:0000250}.;
- Pathway
- Preimplantation Embryo
(Consensus)
Haploinsufficiency Scores
- pHI
- 0.147
- hipred
- Y
- hipred_score
- 0.837
- ghis
- 0.547
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.795
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Sox8
- Phenotype
- growth/size/body region phenotype; endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); skeleton phenotype; reproductive system phenotype; limbs/digits/tail phenotype;
Gene ontology
- Biological process
- osteoblast differentiation;in utero embryonic development;neural crest cell migration;morphogenesis of an epithelium;signal transduction;spermatogenesis;central nervous system development;peripheral nervous system development;male gonad development;regulation of hormone levels;positive regulation of gliogenesis;positive regulation of osteoblast proliferation;skeletal muscle cell differentiation;negative regulation of apoptotic process;cell fate commitment;fat cell differentiation;negative regulation of myoblast differentiation;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;negative regulation of photoreceptor cell differentiation;cell maturation;enteric nervous system development;oligodendrocyte differentiation;Sertoli cell development;astrocyte fate commitment;retina development in camera-type eye;retinal rod cell differentiation;adipose tissue development;morphogenesis of a branching epithelium;renal vesicle induction;ureter morphogenesis;metanephric nephron tubule formation;positive regulation of kidney development;positive regulation of branching involved in ureteric bud morphogenesis
- Cellular component
- nucleus;cytoplasm;nuclear transcription factor complex
- Molecular function
- RNA polymerase II core 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 binding;protein heterodimerization activity