SALL2
spalt like transcription factor 2, the group of Zinc fingers C2H2-type
Basic information
Region (hg38): 14:21521079-21537216
Links
Phenotypes
GenCC
Source:
- coloboma, ocular, autosomal recessive (Limited), mode of inheritance: AR
- coloboma, ocular, autosomal recessive (Limited), mode of inheritance: Unknown
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Coloboma, ocular, autosomal recessive | AR | 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 | 24412933 |
ClinVar
This is a list of variants' phenotypes submitted to
- not provided (30 variants)
- Inborn genetic diseases (21 variants)
- Coloboma, ocular, autosomal recessive (3 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SALL2 gene is commonly pathogenic or not.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 5 | 6 | 11 | |||
missense | 28 | 10 | 38 | |||
nonsense | 1 | 1 | ||||
start loss | 0 | |||||
frameshift | 1 | 1 | ||||
inframe indel | 0 | |||||
splice variant | 0 | |||||
non coding | 2 | 2 | ||||
Total | 1 | 0 | 29 | 5 | 18 |
Variants in SALL2
This is a list of pathogenic ClinVar variants found in the SALL2 region.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
14-21522760-T-C | Inborn genetic diseases | Uncertain significance (Oct 27, 2022) | ||
14-21522763-A-G | Benign (Sep 23, 2022) | |||
14-21522777-G-A | Uncertain significance (Sep 23, 2022) | |||
14-21522814-G-A | Inborn genetic diseases | Uncertain significance (Aug 04, 2023) | ||
14-21522874-G-A | Inborn genetic diseases | Uncertain significance (Aug 02, 2022) | ||
14-21522987-T-C | Uncertain significance (Apr 06, 2022) | |||
14-21523010-C-A | Inborn genetic diseases | Uncertain significance (Jun 28, 2022) | ||
14-21523010-C-G | Benign (Oct 03, 2022) | |||
14-21523209-G-C | Benign (May 28, 2022) | |||
14-21523215-G-A | Benign (Mar 04, 2022) | |||
14-21523249-T-C | Inborn genetic diseases | Uncertain significance (Jul 19, 2022) | ||
14-21523281-G-A | Inborn genetic diseases | Uncertain significance (Oct 03, 2022) | ||
14-21523291-C-T | Inborn genetic diseases | Uncertain significance (Dec 06, 2022) | ||
14-21523427-TTCCTCC-T | Coloboma, ocular, autosomal recessive | Uncertain significance (Mar 27, 2020) | ||
14-21523455-G-C | Benign (Aug 16, 2022) | |||
14-21523458-G-A | Inborn genetic diseases | Uncertain significance (Jun 21, 2023) | ||
14-21523459-A-G | Uncertain significance (Mar 10, 2022) | |||
14-21523492-G-C | Benign (Oct 30, 2022) | |||
14-21523492-G-G | Benign (Nov 01, 2022) | |||
14-21523496-C-T | Benign (Oct 17, 2022) | |||
14-21523516-C-T | Inborn genetic diseases | Uncertain significance (Sep 01, 2021) | ||
14-21523596-C-T | Inborn genetic diseases | Uncertain significance (Nov 10, 2022) | ||
14-21523604-C-T | Benign (Oct 08, 2022) | |||
14-21523670-A-G | Benign (Jul 26, 2022) | |||
14-21523695-A-G | Inborn genetic diseases | Uncertain significance (Mar 29, 2022) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SALL2 | protein_coding | protein_coding | ENST00000327430 | 2 | 16119 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.000138 | 0.998 | 125711 | 0 | 37 | 125748 | 0.000147 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.715 | 527 | 575 | 0.916 | 0.0000313 | 6439 |
Missense in Polyphen | 224 | 294.84 | 0.75974 | 3350 | ||
Synonymous | -0.842 | 255 | 238 | 1.07 | 0.0000134 | 2228 |
Loss of Function | 2.76 | 11 | 26.3 | 0.418 | 0.00000138 | 321 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000429 | 0.000428 |
Ashkenazi Jewish | 0.000523 | 0.000496 |
East Asian | 0.000272 | 0.000163 |
Finnish | 0.000139 | 0.000139 |
European (Non-Finnish) | 0.000106 | 0.000105 |
Middle Eastern | 0.000272 | 0.000163 |
South Asian | 0.0000656 | 0.0000653 |
Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Probable transcription factor that plays a role in eye development before, during, and after optic fissure closure. {ECO:0000269|PubMed:24412933}.;
- Disease
- DISEASE: Coloboma, ocular, autosomal recessive (COAR) [MIM:216820]: An ocular anomaly resulting from abnormal morphogenesis of the optic cup and stalk, and incomplete fusion of the fetal intra-ocular fissure during gestation. The clinical presentation is variable. Some individuals may present with minimal defects in the anterior iris leaf without other ocular defects. More complex malformations create a combination of iris, uveoretinal and/or optic nerve defects without or with microphthalmia or even anophthalmia. {ECO:0000269|PubMed:24412933}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Intolerance Scores
- loftool
- 0.659
- rvis_EVS
- 0.5
- rvis_percentile_EVS
- 79.64
Haploinsufficiency Scores
- pHI
- 0.932
- hipred
- N
- hipred_score
- 0.144
- ghis
- 0.523
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.607
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | High |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Sall2
- 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); renal/urinary system phenotype; embryo 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); normal phenotype;
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;eye development;regulation of transcription, DNA-templated;neural tube development;positive regulation of transcription by RNA polymerase II
- Cellular component
- nucleus
- Molecular function
- RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription activator activity, RNA polymerase II-specific;protein binding;protein-containing complex binding;metal ion binding