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GeneBe

SALL3

spalt like transcription factor 3, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 18:78979817-79002677

Links

ENSG00000256463NCBI:27164OMIM:605079HGNC:10527Uniprot:Q9BXA9AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SALL3 gene.

  • Inborn genetic diseases (97 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.

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
3
clinvar
1
clinvar
4
missense
86
clinvar
12
clinvar
98
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 86 15 1

Variants in SALL3

This is a list of pathogenic ClinVar variants found in the SALL3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
18-78980330-T-C Inborn genetic diseases Likely benign (Apr 07, 2023)2516886
18-78980335-C-T Inborn genetic diseases Uncertain significance (Apr 25, 2023)2540266
18-78992096-G-C Inborn genetic diseases Likely benign (May 25, 2022)2404723
18-78992145-G-T Inborn genetic diseases Uncertain significance (Jul 12, 2023)2611657
18-78992160-T-C Inborn genetic diseases Uncertain significance (Aug 17, 2022)2393310
18-78992212-C-G Inborn genetic diseases Uncertain significance (Feb 10, 2022)2394568
18-78992235-G-A Inborn genetic diseases Uncertain significance (May 09, 2023)2543072
18-78992235-G-T Inborn genetic diseases Uncertain significance (Jul 12, 2023)2610833
18-78992265-G-A Inborn genetic diseases Uncertain significance (Aug 23, 2021)2246602
18-78992436-C-G Inborn genetic diseases Uncertain significance (Nov 29, 2021)2403351
18-78992443-C-T Inborn genetic diseases Uncertain significance (Dec 19, 2022)2336795
18-78992451-C-T Inborn genetic diseases Uncertain significance (May 15, 2023)2546445
18-78992460-C-G Inborn genetic diseases Likely benign (Aug 11, 2022)2344434
18-78992464-C-T Inborn genetic diseases Uncertain significance (Jun 24, 2022)2228405
18-78992521-C-T Inborn genetic diseases Uncertain significance (Dec 01, 2022)2224983
18-78992538-C-G Inborn genetic diseases Uncertain significance (Oct 05, 2021)2253137
18-78992542-G-A Inborn genetic diseases Uncertain significance (Jul 27, 2022)2405656
18-78992546-G-A Likely benign (Oct 09, 2018)754090
18-78992599-C-A Inborn genetic diseases Uncertain significance (Jul 14, 2023)2600101
18-78992710-C-T Inborn genetic diseases Uncertain significance (Jul 14, 2021)2237659
18-78992722-C-T Inborn genetic diseases Uncertain significance (Jul 28, 2021)2239810
18-78992728-C-T Inborn genetic diseases Uncertain significance (Jan 10, 2022)2388319
18-78992743-C-G Inborn genetic diseases Uncertain significance (Oct 03, 2022)2315074
18-78992754-C-G Inborn genetic diseases Uncertain significance (Aug 12, 2021)2205167
18-78992770-G-C Inborn genetic diseases Uncertain significance (Aug 11, 2022)2344435

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SALL3protein_codingprotein_codingENST00000537592 322403
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.4030.5971256700751257450.000298
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.3107567800.9690.00005768239
Missense in Polyphen216300.730.718252843
Synonymous-2.664583911.170.00003562734
Loss of Function3.74627.00.2230.00000125324

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0008090.000750
Ashkenazi Jewish0.000.00
East Asian0.0001680.000163
Finnish0.0001670.000139
European (Non-Finnish)0.0002780.000255
Middle Eastern0.0001680.000163
South Asian0.0006860.000686
Other0.0001630.000163

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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