SALL2
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
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.
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 | 15 | 20 | ||||
missense | 64 | 10 | 82 | |||
nonsense | 1 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 2 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 2 | |||||
Total | 0 | 0 | 66 | 24 | 17 |
Variants in SALL2
This is a list of pathogenic ClinVar variants found in the SALL2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
14-21522047-G-A | SALL2-related disorder | Likely benign (Mar 27, 2019) | ||
14-21522208-T-G | SALL2-related disorder | Likely benign (Jul 06, 2020) | ||
14-21522738-G-T | not specified | Uncertain significance (Feb 28, 2024) | ||
14-21522760-T-C | not specified | Uncertain significance (Oct 27, 2022) | ||
14-21522763-A-G | SALL2-related disorder | Benign/Likely benign (Nov 13, 2023) | ||
14-21522777-G-A | not specified | Uncertain significance (Dec 27, 2023) | ||
14-21522814-G-A | not specified | Uncertain significance (Aug 04, 2023) | ||
14-21522815-G-A | SALL2-related disorder | Likely benign (Mar 25, 2019) | ||
14-21522831-A-T | not specified | Uncertain significance (Jun 17, 2024) | ||
14-21522870-G-T | Uncertain significance (Jun 30, 2023) | |||
14-21522874-G-A | not specified | Uncertain significance (Aug 02, 2022) | ||
14-21522915-G-A | not specified | Uncertain significance (Jun 17, 2024) | ||
14-21522987-T-C | Uncertain significance (Apr 06, 2022) | |||
14-21523010-C-A | not specified | Uncertain significance (Jun 28, 2022) | ||
14-21523010-C-G | SALL2-related disorder | Benign (Jan 25, 2024) | ||
14-21523101-G-A | not specified | Uncertain significance (Jun 17, 2024) | ||
14-21523209-G-C | Benign (Jan 31, 2024) | |||
14-21523215-G-A | SALL2-related disorder | Benign (Jul 12, 2023) | ||
14-21523249-T-C | not specified | Uncertain significance (Jul 19, 2022) | ||
14-21523280-C-T | Likely benign (May 17, 2023) | |||
14-21523281-G-A | not specified | Uncertain significance (Oct 03, 2022) | ||
14-21523291-C-T | not specified | Uncertain significance (Dec 06, 2022) | ||
14-21523427-TTCCTCC-T | Coloboma, ocular, autosomal recessive | Uncertain significance (Mar 27, 2020) | ||
14-21523428-T-C | not specified | Uncertain significance (May 10, 2024) | ||
14-21523455-G-C | Benign (Jul 03, 2023) |
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