SALL3
Basic information
Region (hg38): 18:78979818-79002677
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (263 variants)
- not_provided (4 variants)
- Anophthalmia-microphthalmia_syndrome (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SALL3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000171999.4. 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 | 5 | |||||
missense | 245 | 18 | 263 | |||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 245 | 22 | 1 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SALL3 | protein_coding | protein_coding | ENST00000537592 | 3 | 22403 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.403 | 0.597 | 125670 | 0 | 75 | 125745 | 0.000298 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.310 | 756 | 780 | 0.969 | 0.0000576 | 8239 |
Missense in Polyphen | 216 | 300.73 | 0.71825 | 2843 | ||
Synonymous | -2.66 | 458 | 391 | 1.17 | 0.0000356 | 2734 |
Loss of Function | 3.74 | 6 | 27.0 | 0.223 | 0.00000125 | 324 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000809 | 0.000750 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.000168 | 0.000163 |
Finnish | 0.000167 | 0.000139 |
European (Non-Finnish) | 0.000278 | 0.000255 |
Middle Eastern | 0.000168 | 0.000163 |
South Asian | 0.000686 | 0.000686 |
Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Probable transcription factor.;
Recessive Scores
- pRec
- 0.121
Haploinsufficiency Scores
- pHI
- 0.534
- hipred
- Y
- hipred_score
- 0.806
- ghis
- 0.500
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.307
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Sall3
- Phenotype
- craniofacial phenotype; homeostasis/metabolism phenotype; growth/size/body region 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); digestive/alimentary phenotype; skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system 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);
Gene ontology
- Biological process
- regulation of transcription, DNA-templated;regulation of transcription by RNA polymerase II;olfactory bulb interneuron development;forelimb morphogenesis;hindlimb morphogenesis;negative regulation of smoothened signaling pathway
- Cellular component
- nucleus
- Molecular function
- DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;metal ion binding