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.

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	1	4
missense			114	14		128
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	114	17	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
18-78980319-C-G		not specified	Uncertain significance (Dec 13, 2023)
18-78980330-T-C		not specified	Likely benign (Apr 07, 2023)
18-78980335-C-T		not specified	Uncertain significance (Apr 25, 2023)
18-78992096-G-C		not specified	Likely benign (May 25, 2022)
18-78992109-G-C		not specified	Uncertain significance (May 06, 2024)
18-78992145-G-T		not specified	Uncertain significance (Jul 12, 2023)
18-78992160-T-C		not specified	Uncertain significance (Aug 17, 2022)
18-78992167-A-C		not specified	Uncertain significance (Mar 07, 2024)
18-78992181-G-A		not specified	Likely benign (Apr 01, 2024)
18-78992190-C-A		not specified	Uncertain significance (Oct 25, 2023)
18-78992208-T-A		not specified	Uncertain significance (Jun 18, 2024)
18-78992212-C-G		not specified	Uncertain significance (Feb 10, 2022)
18-78992235-G-A		not specified	Uncertain significance (May 09, 2023)
18-78992235-G-T		not specified	Uncertain significance (Jul 12, 2023)
18-78992265-G-A		not specified	Uncertain significance (Aug 23, 2021)
18-78992321-G-C		not specified	Uncertain significance (Jan 23, 2024)
18-78992436-C-G		not specified	Uncertain significance (Nov 29, 2021)
18-78992443-C-T		not specified	Uncertain significance (Dec 19, 2022)
18-78992451-C-T		not specified	Uncertain significance (May 15, 2023)
18-78992460-C-G		not specified	Likely benign (Aug 11, 2022)
18-78992464-C-T		not specified	Uncertain significance (Jun 24, 2022)
18-78992521-C-T		not specified	Uncertain significance (Dec 01, 2022)
18-78992538-C-G		not specified	Uncertain significance (Oct 05, 2021)
18-78992542-G-A		not specified	Uncertain significance (Jul 27, 2022)
18-78992546-G-A			Likely benign (Oct 09, 2018)

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