SALL1 p.Pro799=
c.2397C>T · rs752496655 · VCV3058240
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0111%, eas)
Conditions
1
Townes-Brocks syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.8 | GERP -4.2 |
| Overall | ||
| CADD | 0.654 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0111%
East Asian · 5/44,888 alleles
Filtering AF
0.00434%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00276%
Overall
0.00142%
23/1,614,154 alleles · ultra-rare
exomes 23/1,461,886 · genomes 0/152,268 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0111% | 8,978 |
| South Asian | 0.00329% | 30,361 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,250 |
| African / African-American | 0.00133% | 75,034 |
| European (non-Finnish) | 0.00102% | 98,335 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- SALL1
- Protein
- p.Pro799=
- Coding
- c.2397C>T
- MANE Select
- NM_002968
- dbSNP
- rs752496655
- Type
- single nucleotide variant
- Location
- chr16:51139825 (GRCh38)
- Gene constraint
- LOEUF 0.228 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 49.54
- Residue 799
- the 'disordered' region
Similar variants
- SALL1 p.Arg1054Ter Pathogenic/Likely pathogenic ★★ same condition
- SALL1 p.Arg276Ter Pathogenic/Likely pathogenic ★★ same condition
- SALL1 p.Arg786Ter Pathogenic ★★ same condition
- SALL1 p.Gln272Ter Pathogenic ★★ same condition
- SALL1 p.Gln291Ter Pathogenic/Likely pathogenic ★★ same condition
- SALL1 p.Gln323Ter Pathogenic ★★ same condition
- SALL1 p.Ala369Val Uncertain significance ★★ ⚠ same condition
- SALL1 p.Ala637Val Uncertain significance ★★ ⚠ same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/sall1-p-pro799 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown