SALL3

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

Basic information

Region (hg38): 18:78979818-79002677

Links

ENSG00000256463

∙ NCBI:27164 ∙ OMIM:605079 ∙ HGNC:10527 ∙ Uniprot:Q9BXA9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

not_specified (263 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. These statistics are base on transcript: NM_000171999.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				4 clinvar	1 clinvar	5
missense			245 clinvar	18 clinvar		263
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	245	22	1

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SALL3	protein_coding	protein_coding	ENST00000537592	3	22403

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.403	0.597	125670	0	75	125745	0.000298

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.310	756	780	0.969	0.0000576	8239
Missense in Polyphen		216	300.73	0.71825		2843
Synonymous	-2.66	458	391	1.17	0.0000356	2734
Loss of Function	3.74	6	27.0	0.223	0.00000125	324

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000809	0.000750
Ashkenazi Jewish	0.00	0.00
East Asian	0.000168	0.000163
Finnish	0.000167	0.000139
European (Non-Finnish)	0.000278	0.000255
Middle Eastern	0.000168	0.000163
South Asian	0.000686	0.000686
Other	0.000163	0.000163

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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

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