SALL2

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

Basic information

Region (hg38): 14:21521079-21537216

Links

ENSG00000165821 ∙ NCBI:6297 ∙ OMIM:602219 ∙ HGNC:10526 ∙ Uniprot:Q9Y467 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

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

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Coloboma, ocular, autosomal recessive	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Ophthalmologic	24412933

ClinVar

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

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				15	5	20
missense			64	8	10	82
nonsense				1		1
start loss						0
frameshift						0
inframe indel			2			2
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					2	2
Total	0	0	66	24	17

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 disorder	Likely benign (Mar 27, 2019)
14-21522208-T-G		SALL2-related disorder	Likely benign (Jul 06, 2020)
14-21522738-G-T		not specified	Uncertain significance (Feb 28, 2024)
14-21522760-T-C		not specified	Uncertain significance (Oct 27, 2022)
14-21522763-A-G		SALL2-related disorder	Benign/Likely benign (Nov 13, 2023)
14-21522777-G-A		not specified	Uncertain significance (Dec 27, 2023)
14-21522814-G-A		not specified	Uncertain significance (Aug 04, 2023)
14-21522815-G-A		SALL2-related disorder	Likely benign (Mar 25, 2019)
14-21522870-G-T			Uncertain significance (Jun 30, 2023)
14-21522874-G-A		not specified	Uncertain significance (Aug 02, 2022)
14-21522987-T-C			Uncertain significance (Apr 06, 2022)
14-21523010-C-A		not specified	Uncertain significance (Jun 28, 2022)
14-21523010-C-G		SALL2-related disorder	Benign (Jan 25, 2024)
14-21523209-G-C			Benign (Jan 31, 2024)
14-21523215-G-A		SALL2-related disorder	Benign (Jul 12, 2023)
14-21523249-T-C		not specified	Uncertain significance (Jul 19, 2022)
14-21523280-C-T			Likely benign (May 17, 2023)
14-21523281-G-A		not specified	Uncertain significance (Oct 03, 2022)
14-21523291-C-T		not specified	Uncertain significance (Dec 06, 2022)
14-21523427-TTCCTCC-T		Coloboma, ocular, autosomal recessive	Uncertain significance (Mar 27, 2020)
14-21523455-G-C			Benign (Jul 03, 2023)
14-21523458-G-A		not specified	Uncertain significance (Jun 21, 2023)
14-21523459-A-G			Uncertain significance (Mar 10, 2022)
14-21523492-G-C			Benign (Jan 31, 2024)
14-21523492-G-G			Benign (Jan 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SALL2	protein_coding	protein_coding	ENST00000327430	2	16119

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000138	0.998	125711	0	37	125748	0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.715	527	575	0.916	0.0000313	6439
Missense in Polyphen		224	294.84	0.75974		3350
Synonymous	-0.842	255	238	1.07	0.0000134	2228
Loss of Function	2.76	11	26.3	0.418	0.00000138	321

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000429	0.000428
Ashkenazi Jewish	0.000523	0.000496
East Asian	0.000272	0.000163
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000106	0.000105
Middle Eastern	0.000272	0.000163
South Asian	0.0000656	0.0000653
Other	0.000163	0.000163

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

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

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