SALL1 p.Pro130=
c.390G>A · rs75156807 · VCV258872
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 8 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.43%, nfe)
Conditions
1
Townes-Brocks syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -7.7 | GERP -3.9 |
| Overall | ||
| CADD | 6.394 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.43%
European (non-Finnish) · 16,867/1,180,004 alleles
Filtering AF
1.41%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.4%
Overall
1.22%
19,646/1,613,810 alleles · low-frequency
exomes 18,331/1,461,658 · genomes 1,315/152,152 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 1.43% | 70 |
| Ashkenazi Jewishnot grpmax-eligible | 1.19% | 84 |
| Middle Eastern | 1.16% | 86 |
| Remaining individualsnot grpmax-eligible | 1% | 100 |
| Admixed American | 0.811% | 123 |
| Finnishnot grpmax-eligible | 0.784% | 127 |
| South Asian | 0.603% | 166 |
| African / African-American | 0.256% | 391 |
| East Asian | 0.00668% | 14,960 |
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.Pro130=
- Coding
- c.390G>A
- MANE Select
- NM_002968
- dbSNP
- rs75156807
- Type
- single nucleotide variant
- Location
- chr16:51141832 (GRCh38)
- Gene constraint
- LOEUF 0.228 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 49.54
Similar variants
- SALL1 p.Pro130Leu Likely benign ★★ same residue
- SALL1 p.Pro130Ala Uncertain significance ★ ⚠ same residue
- 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
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-pro130 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown