SALL1 p.Pro664=
c.1992G>A · rs754352358 · VCV3048586
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.283%, 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 | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -8.5 | GERP -4.2 |
| Overall | ||
| CADD | 0.501 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.283%
East Asian · 127/44,866 alleles
Filtering AF
0.243%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.228%
Overall
0.011%
177/1,614,144 alleles · rare
exomes 166/1,461,856 · genomes 11/152,288 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.283% | 353 |
| Admixed American | 0.0233% | 4,288 |
| Middle Eastern | 0.0165% | 6,062 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,812 |
| African / African-American | 0.00266% | 37,524 |
| European (non-Finnish) | 0.00195% | 51,306 |
| Finnishnot grpmax-eligible | 0.00156% | 63,994 |
| South Asian | 0.0011% | 91,088 |
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.Pro664=
- Coding
- c.1992G>A
- MANE Select
- NM_002968
- dbSNP
- rs754352358
- Type
- single nucleotide variant
- Location
- chr16:51140230 (GRCh38)
- Gene constraint
- LOEUF 0.228 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 49.54
Similar variants
- SALL1 p.Pro664Leu Conflicting classifications of pathogenicity ★ 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
- SALL1 p.Ala369Val 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-pro664 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown