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GeneBe

SALL1

spalt like transcription factor 1, the group of Zinc fingers C2H2-type

Basic information

Region (hg38): 16:51135981-51152334

Previous symbols: [ "TBS" ]

Links

ENSG00000103449NCBI:6299OMIM:602218HGNC:10524Uniprot:Q9NSC2AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • Townes-Brocks syndrome 1 (Strong), mode of inheritance: AD
  • Townes-Brocks syndrome 1 (Definitive), mode of inheritance: AD
  • Townes-Brocks syndrome (Supportive), mode of inheritance: AD
  • Townes-Brocks syndrome 1 (Definitive), mode of inheritance: AD
  • Townes-Brocks syndrome 1 (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Townes-Brocks syndrome 1ADAudiologic/Otolaryngologic; Cardiovascular; Endocrine; RenalWhile frequently recognizable, early recognition and treatment of hearing impairment may improve outcomes, including speech and language development; Surveillance for manifestations affecting other organ systems (eg, cardiac, endocrine, and renal) may allow early intervention, potentially reducing morbidity and mortalityAudiologic/Otolaryngologic; Cardiovascular; Craniofacial; Endocrine; Gastrointestinal; Genitourinary; Musculoskeletal; Renal5042490; 9072124; 9425907; 10928856; 11484202; 14755477; 16088922; 8000979; 17431915; 20301618
The condition may be recognizable due to the presence of a specific pattern of congenital malformations affecting hearing as well as multiple organ systems

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SALL1 gene.

  • Townes syndrome (215 variants)
  • not provided (194 variants)
  • Townes-Brocks syndrome 1 (104 variants)
  • Inborn genetic diseases (54 variants)
  • not specified (49 variants)
  • SALL1-related condition (11 variants)
  • Congenital anomaly of kidney and urinary tract (3 variants)
  • VACTERL with hydrocephalus (1 variants)
  • Microcephaly (1 variants)
  • Townes-Brocks-branchiootorenal-like syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SALL1 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
4
clinvar
67
clinvar
12
clinvar
83
missense
1
clinvar
167
clinvar
28
clinvar
9
clinvar
205
nonsense
19
clinvar
4
clinvar
1
clinvar
24
start loss
0
frameshift
27
clinvar
6
clinvar
33
inframe indel
7
clinvar
6
clinvar
1
clinvar
14
splice donor/acceptor (+/-2bp)
0
splice region
1
2
3
non coding
3
clinvar
9
clinvar
8
clinvar
20
Total 46 11 182 110 30

Highest pathogenic variant AF is 0.0000131

Variants in SALL1

This is a list of pathogenic ClinVar variants found in the SALL1 region.

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

Position Type Phenotype Significance ClinVar
16-51135999-C-CA Townes-Brocks syndrome 1 Likely benign (Jun 14, 2016)319575
16-51136078-A-AC Townes-Brocks syndrome 1 Uncertain significance (Jun 14, 2016)319576
16-51136183-CAAG-C Townes-Brocks syndrome 1 Conflicting classifications of pathogenicity (Apr 01, 2023)319579
16-51136405-CTT-C Townes-Brocks syndrome 1 Uncertain significance (Jun 14, 2016)319583
16-51136523-CA-C Townes-Brocks syndrome 1 Benign (Jun 14, 2016)319586
16-51136548-TA-T Townes-Brocks syndrome 1 Uncertain significance (Jun 14, 2016)319587
16-51137019-AGGGGC-A Townes-Brocks syndrome 1 Likely benign (Mar 31, 2019)319593
16-51137019-A-AGGGGC Benign (Mar 03, 2015)1249227
16-51137103-C-T SALL1-related condition Likely benign (Aug 13, 2019)3052886
16-51137121-G-A Townes syndrome Likely benign (Dec 21, 2022)2794936
16-51137123-C-T Townes syndrome • Inborn genetic diseases Conflicting classifications of pathogenicity (Nov 07, 2022)808043
16-51137124-G-A Townes syndrome Likely benign (Apr 07, 2023)2722026
16-51137124-G-C Benign (Oct 14, 2020)1280309
16-51137130-C-T Townes syndrome Likely benign (Jul 14, 2021)711990
16-51137140-T-C Inborn genetic diseases Uncertain significance (Oct 06, 2021)2254095
16-51137145-G-A Townes syndrome • not specified • Townes-Brocks syndrome 1 • SALL1-related condition Benign/Likely benign (Jan 15, 2024)319597
16-51137149-C-T Townes syndrome • Inborn genetic diseases Conflicting classifications of pathogenicity (Jan 01, 2023)426902
16-51137150-G-A Townes syndrome Uncertain significance (Jun 04, 2022)2059678
16-51137159-G-A Townes syndrome Uncertain significance (May 01, 2023)2970483
16-51137172-G-A not specified • Townes syndrome Benign (Dec 02, 2023)287591
16-51137197-A-C Townes syndrome • Inborn genetic diseases • SALL1-related condition Uncertain significance (Sep 20, 2023)1415730
16-51137201-C-T Inborn genetic diseases Uncertain significance (Dec 27, 2023)3157556
16-51137212-G-T Inborn genetic diseases Uncertain significance (Jun 07, 2023)2558700
16-51137215-T-C not specified • Townes-Brocks syndrome 1 • Townes syndrome Benign/Likely benign (Jan 22, 2024)218510
16-51137219-G-A Inborn genetic diseases Uncertain significance (Mar 17, 2023)2526254

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SALL1protein_codingprotein_codingENST00000251020 315393
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.000.000295125741071257480.0000278
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.7226877420.9250.00004558724
Missense in Polyphen163241.760.674232936
Synonymous-0.5043313201.040.00002322732
Loss of Function4.92232.10.06230.00000178406

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.000.00
Finnish0.00004620.0000462
European (Non-Finnish)0.00004480.0000439
Middle Eastern0.000.00
South Asian0.00003270.0000327
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Transcriptional repressor involved in organogenesis. {ECO:0000250}.;
Disease
DISEASE: Townes-Brocks syndrome 1 (TBS1) [MIM:107480]: A form of Townes-Brocks syndrome, a rare autosomal dominant disease characterized by the triad of imperforate anus, dysplastic ears, and thumb malformations. Minor features of the condition include hearing loss, foot malformations, renal impairment with or without renal malformations, genitourinary malformations, and congenital heart disease. {ECO:0000269|PubMed:10533063, ECO:0000269|PubMed:9425907, ECO:0000269|PubMed:9973281}. Note=The disease is caused by mutations affecting the gene represented in this entry. Some individuals with SALL1 mutations manifest a phenotype overlapping with TBS1 and bronchio-oto-renal syndrome. Clinical features include dysplastic ears, hypoplastic kidneys with impaired renal function, gastroesophageal reflux, hypermetropia, hypospadias, and mild developmental delay. Affected individuals lack the characteristic anal or hand malformations of TBS1. {ECO:0000269|PubMed:10928856}.;
Pathway
POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation;Olfactory bulb development and olfactory learning;Developmental Biology;POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferation;Transcriptional regulation of pluripotent stem cells (Consensus)

Recessive Scores

pRec
0.278

Intolerance Scores

loftool
0.0480
rvis_EVS
-0.83
rvis_percentile_EVS
11.53

Haploinsufficiency Scores

pHI
0.933
hipred
Y
hipred_score
0.852
ghis
0.502

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
S
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.311

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Sall1
Phenotype
cellular phenotype; normal 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); growth/size/body region phenotype; limbs/digits/tail 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); hearing/vestibular/ear phenotype; digestive/alimentary phenotype; skeleton phenotype; renal/urinary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype;

Gene ontology

Biological process
negative regulation of transcription by RNA polymerase II;ureteric bud development;branching involved in ureteric bud morphogenesis;kidney development;ventricular septum development;mesenchymal to epithelial transition involved in metanephros morphogenesis;regulation of transcription, DNA-templated;heart development;gonad development;histone deacetylation;olfactory nerve development;olfactory bulb interneuron differentiation;pituitary gland development;positive regulation of Wnt signaling pathway;adrenal gland development;inductive cell-cell signaling;somatic stem cell population maintenance;outer ear morphogenesis;embryonic digit morphogenesis;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;embryonic digestive tract development;limb development;olfactory bulb mitral cell layer development;kidney epithelium development;ureteric bud invasion
Cellular component
heterochromatin;nucleus;nucleoplasm;cytoplasm;chromocenter
Molecular function
RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;DNA binding;DNA-binding transcription factor activity;histone deacetylase activity;protein binding;beta-catenin binding;metal ion binding