SIX6
Basic information
Region (hg38): 14:60509146-60512850
Previous symbols: [ "OPTX2" ]
Links
Phenotypes
GenCC
Source:
- colobomatous optic disc-macular atrophy-chorioretinopathy syndrome (Limited), mode of inheritance: AD
- colobomatous optic disc-macular atrophy-chorioretinopathy syndrome (Strong), mode of inheritance: AR
- colobomatous optic disc-macular atrophy-chorioretinopathy syndrome (Strong), mode of inheritance: AR
- colobomatous optic disc-macular atrophy-chorioretinopathy syndrome (Supportive), mode of inheritance: AR
- colobomatous optic disc-macular atrophy-chorioretinopathy syndrome (Limited), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Microphthalmia, isolated, with cataract 2; Optic disc anomalies with retinal and/or macular dystrophy | AD | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Ophthalmologic | 15266624; 23167593; 24702266 |
ClinVar
This is a list of variants' phenotypes submitted to
- Sclerocornea;Developmental cataract;Cornea plana;Microphthalmia (1 variants)
- Nystagmus;Developmental cataract;Microcornea;Sclerocornea (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SIX6 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 | 28 | 32 | ||||
| missense | 42 | 46 | ||||
| nonsense | 3 | |||||
| start loss | 1 | |||||
| frameshift | 4 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 2 | 2 | ||||
| non coding | 11 | 20 | ||||
| Total | 2 | 4 | 60 | 35 | 5 |
Variants in SIX6
This is a list of pathogenic ClinVar variants found in the SIX6 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SIX6 | protein_coding | protein_coding | ENST00000327720 | 2 | 3900 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.518 | 0.479 | 125730 | 0 | 12 | 125742 | 0.0000477 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.714 | 117 | 141 | 0.831 | 0.00000634 | 1550 |
| Missense in Polyphen | 30 | 50.409 | 0.59514 | 564 | ||
| Synonymous | 0.938 | 55 | 64.6 | 0.852 | 0.00000303 | 529 |
| Loss of Function | 2.44 | 2 | 10.6 | 0.189 | 4.75e-7 | 100 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000155 | 0.000148 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000110 | 0.000109 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000448 | 0.0000440 |
| Middle Eastern | 0.000110 | 0.000109 |
| South Asian | 0.0000328 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: May be involved in eye development.;
- Pathway
- Ectoderm Differentiation
(Consensus)
Recessive Scores
- pRec
- 0.125
Intolerance Scores
- loftool
- 0.223
- rvis_EVS
- 0.68
- rvis_percentile_EVS
- 84.93
Haploinsufficiency Scores
- pHI
- 0.313
- hipred
- Y
- hipred_score
- 0.837
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.928
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Six6
- Phenotype
- endocrine/exocrine gland 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;
Zebrafish Information Network
- Gene name
- six6b
- Affected structure
- mandibular arch skeleton
- Phenotype tag
- abnormal
- Phenotype quality
- shortened
Gene ontology
- Biological process
- eye development;visual perception;animal organ morphogenesis;negative regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;anatomical structure development
- Cellular component
- nucleus;transcription factor complex
- Molecular function
- transcription regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific