SOX12
Basic information
Region (hg38): 20:325551-330224
Previous symbols: [ "SOX22" ]
Links
Phenotypes
GenCC
Source:
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 SOX12 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 | 2 | |||||
missense | 24 | 25 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 24 | 0 | 3 |
Variants in SOX12
This is a list of pathogenic ClinVar variants found in the SOX12 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
20-325967-C-T | not specified | Uncertain significance (Jun 17, 2022) | ||
20-325971-C-T | not specified | Uncertain significance (Jan 03, 2024) | ||
20-325991-G-A | not specified | Uncertain significance (Aug 12, 2021) | ||
20-326271-A-T | not specified | Uncertain significance (Oct 12, 2021) | ||
20-326276-G-T | not specified | Uncertain significance (Oct 14, 2021) | ||
20-326277-C-A | not specified | Uncertain significance (Jul 05, 2023) | ||
20-326342-C-T | not specified | Uncertain significance (May 16, 2024) | ||
20-326357-C-T | not specified | Uncertain significance (Sep 06, 2022) | ||
20-326402-G-A | not specified | Uncertain significance (May 16, 2024) | ||
20-326414-G-T | not specified | Uncertain significance (Jun 06, 2023) | ||
20-326475-G-C | not specified | Uncertain significance (Dec 05, 2022) | ||
20-326499-C-A | not specified | Uncertain significance (Dec 07, 2021) | ||
20-326523-C-G | not specified | Uncertain significance (Jan 20, 2023) | ||
20-326528-C-G | not specified | Uncertain significance (Feb 07, 2023) | ||
20-326535-A-G | not specified | Uncertain significance (Apr 13, 2022) | ||
20-326546-G-C | not specified | Uncertain significance (Jun 22, 2023) | ||
20-326555-G-A | not specified | Uncertain significance (Jan 12, 2024) | ||
20-326560-C-G | Benign (Feb 09, 2018) | |||
20-326570-G-C | not specified | Uncertain significance (Sep 16, 2021) | ||
20-326622-A-C | not specified | Uncertain significance (Nov 21, 2022) | ||
20-326637-A-C | not specified | Uncertain significance (Aug 31, 2022) | ||
20-326643-G-C | not specified | Uncertain significance (Aug 01, 2022) | ||
20-326652-A-G | Benign (Jan 31, 2018) | |||
20-326655-C-T | not specified | Uncertain significance (Nov 29, 2021) | ||
20-326656-G-A | Benign (Dec 19, 2017) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SOX12 | protein_coding | protein_coding | ENST00000342665 | 1 | 4659 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.856 | 0.142 | 0 | 0 | 0 | 0 | 0.00 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.79 | 78 | 137 | 0.570 | 0.00000637 | 1975 |
Missense in Polyphen | 8 | 28.294 | 0.28275 | 328 | ||
Synonymous | 0.417 | 59 | 63.2 | 0.933 | 0.00000306 | 671 |
Loss of Function | 2.34 | 0 | 6.35 | 0.00 | 2.74e-7 | 94 |
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: Binds to the sequence 5'-AACAAT-3'. {ECO:0000250}.;
Haploinsufficiency Scores
- pHI
- 0.287
- hipred
- hipred_score
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.441
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Sox12
- Phenotype
- craniofacial 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); limbs/digits/tail 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; embryo phenotype; skeleton phenotype; immune system phenotype;
Gene ontology
- Biological process
- regulation of transcription, DNA-templated;regulation of transcription by RNA polymerase II;spinal cord development;cell differentiation;cell fate commitment;positive regulation of transcription by RNA polymerase II;protein-DNA complex assembly
- Cellular component
- cellular_component;nucleus;nucleoplasm;protein-DNA complex;nuclear transcription factor complex
- Molecular function
- transcription regulatory region 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 coactivator activity