Menu
GeneBe

SALL2

spalt like transcription factor 2, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 14:21521079-21537216

Links

ENSG00000165821NCBI:6297OMIM:602219HGNC:10526Uniprot:Q9Y467AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • coloboma, ocular, autosomal recessive (Limited), mode of inheritance: AR
  • coloboma, ocular, autosomal recessive (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Coloboma, ocular, autosomal recessiveARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingOphthalmologic24412933

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SALL2 gene.

  • not provided (38 variants)
  • Inborn genetic diseases (33 variants)
  • Coloboma, ocular, autosomal recessive (2 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.

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
8
clinvar
6
clinvar
14
missense
41
clinvar
4
clinvar
10
clinvar
55
nonsense
0
start loss
0
frameshift
0
inframe indel
1
clinvar
1
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
2
clinvar
2
Total 0 0 42 12 18

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 condition Likely benign (Mar 27, 2019)3046285
14-21522208-T-G SALL2-related condition Likely benign (Jul 06, 2020)3033477
14-21522760-T-C Inborn genetic diseases Uncertain significance (Oct 27, 2022)2205017
14-21522763-A-G SALL2-related condition Benign/Likely benign (Nov 13, 2023)2056324
14-21522777-G-A Uncertain significance (Dec 27, 2023)1932176
14-21522814-G-A Inborn genetic diseases Uncertain significance (Aug 04, 2023)2616138
14-21522815-G-A SALL2-related condition Likely benign (Mar 25, 2019)3058672
14-21522870-G-T Uncertain significance (Jun 30, 2023)2880878
14-21522874-G-A Inborn genetic diseases Uncertain significance (Aug 02, 2022)2274822
14-21522987-T-C Uncertain significance (Apr 06, 2022)2121915
14-21523010-C-A Inborn genetic diseases Uncertain significance (Jun 28, 2022)2233459
14-21523010-C-G SALL2-related condition Benign (Jan 25, 2024)2040752
14-21523209-G-C Benign (Jan 31, 2024)784278
14-21523215-G-A SALL2-related condition Benign (Jul 12, 2023)739905
14-21523249-T-C Inborn genetic diseases Uncertain significance (Jul 19, 2022)2386167
14-21523280-C-T Likely benign (May 17, 2023)2920198
14-21523281-G-A Inborn genetic diseases Uncertain significance (Oct 03, 2022)2403057
14-21523291-C-T Inborn genetic diseases Uncertain significance (Dec 06, 2022)2211800
14-21523427-TTCCTCC-T Coloboma, ocular, autosomal recessive Uncertain significance (Mar 27, 2020)2435647
14-21523455-G-C Benign (Jul 03, 2023)2154876
14-21523458-G-A Inborn genetic diseases Uncertain significance (Jun 21, 2023)2604922
14-21523459-A-G Uncertain significance (Mar 10, 2022)2067346
14-21523492-G-C Benign (Jan 31, 2024)769203
14-21523492-G-G Benign (Jan 29, 2024)1561535
14-21523496-C-T Benign (Jan 22, 2024)2039674

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SALL2protein_codingprotein_codingENST00000327430 216119
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.0001380.9981257110371257480.000147
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.7155275750.9160.00003136439
Missense in Polyphen224294.840.759743350
Synonymous-0.8422552381.070.00001342228
Loss of Function2.761126.30.4180.00000138321

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0004290.000428
Ashkenazi Jewish0.0005230.000496
East Asian0.0002720.000163
Finnish0.0001390.000139
European (Non-Finnish)0.0001060.000105
Middle Eastern0.0002720.000163
South Asian0.00006560.0000653
Other0.0001630.000163

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumHigh
CancerMediumMediumMedium

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