SALL1

Chr 16

spalt like transcription factor 1

Also known as: HEL-S-89, HSAL1, Sal-1, TBS, ZNF794

NCBI Gene: 6299ENSG00000103449UniProt: Q9NSC2

The protein encoded by this gene is a zinc finger transcriptional repressor and may be part of the NuRD histone deacetylase complex (HDAC). Defects in this gene are a cause of Townes-Brocks syndrome (TBS) as well as bronchio-oto-renal syndrome (BOR). Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

GeneReviewsResearchGenerating clinical summary…

Primary Disease Associations & Inheritance

UniProtTownes-Brocks syndrome 1

Clinical highlights

Gene-disease validity (ClinGen)
Townes-Brocks syndrome 1 · ADDefinitivesufficient evidence for diagnostic panels
Interpreting a novel variant
Loss of function is the curated mechanism (Gene2Phenotype) and the gene is intolerant of it in the population — truncating, frameshift and canonical splice variants carry more prior weight here than missense.Curated gene-level mechanism — a prior for triage, not a per-variant call.
0
Active trials
46
Pubs (1 yr)
—
P/LP submissions
—
P/LP missense
0.20
LOEUF· LoF intol.
LOF
Mechanism· G2P
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GeneReview available — SALL1
Authoritative clinical overview · Recommended first read
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Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint?
0.20LOEUF
pLI 1.000
Z-score 4.92
OE 0.06 (0.02–0.20)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint?
0.72Z-score
OE missense 0.93 (0.87–0.99)
687 obs / 742.3 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?
LoF OE?0.06 (0.02–0.20)
0≤0.351.4
Missense OE?0.93 (0.87–0.99)
0≤0.61.4
Synonymous OE?1.04
0≤1.21.6
LoF obs/exp: 2 / 32.1Missense obs/exp: 687 / 742.3Syn Z: -0.50

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

SALL1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients