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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:Q9Y467AlphaFoldGenCCjaxSfariGnomADPubmed

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 (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)link
14-21522763-A-G Benign (Sep 23, 2022)link
14-21522777-G-A Uncertain significance (Sep 23, 2022)link
14-21522814-G-A Inborn genetic diseases Uncertain significance (Aug 04, 2023)link
14-21522874-G-A Inborn genetic diseases Uncertain significance (Aug 02, 2022)link
14-21522987-T-C Uncertain significance (Apr 06, 2022)link
14-21523010-C-A Inborn genetic diseases Uncertain significance (Jun 28, 2022)link
14-21523010-C-G Benign (Oct 03, 2022)link
14-21523209-G-C Benign (May 28, 2022)link
14-21523215-G-A Benign (Mar 04, 2022)link
14-21523249-T-C Inborn genetic diseases Uncertain significance (Jul 19, 2022)link
14-21523281-G-A Inborn genetic diseases Uncertain significance (Oct 03, 2022)link
14-21523291-C-T Inborn genetic diseases Uncertain significance (Dec 06, 2022)link
14-21523427-TTCCTCC-T Coloboma, ocular, autosomal recessive Uncertain significance (Mar 27, 2020)link
14-21523455-G-C Benign (Aug 16, 2022)link
14-21523458-G-A Inborn genetic diseases Uncertain significance (Jun 21, 2023)link
14-21523459-A-G Uncertain significance (Mar 10, 2022)link
14-21523492-G-C Benign (Oct 30, 2022)link
14-21523492-G-G Benign (Nov 01, 2022)link
14-21523496-C-T Benign (Oct 17, 2022)link
14-21523516-C-T Inborn genetic diseases Uncertain significance (Sep 01, 2021)link
14-21523596-C-T Inborn genetic diseases Uncertain significance (Nov 10, 2022)link
14-21523604-C-T Benign (Oct 08, 2022)link
14-21523670-A-G Benign (Jul 26, 2022)link
14-21523695-A-G Inborn genetic diseases Uncertain significance (Mar 29, 2022)link

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