SALL4 p.Pro28=
c.84G>A · VCV4945404
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0308%, sas)
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 -3.3 | GERP -3.5 |
| Overall | ||
| CADD | 8.803 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0308%
South Asian · 28/90,988 alleles
Filtering AF
0.0218%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0188%
Overall
0.0018%
29/1,610,586 alleles · ultra-rare
exomes 28/1,458,446 · genomes 1/152,140 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0308% | 3,250 |
| Remaining individualsnot grpmax-eligible | 0.00161% | 62,280 |
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
- SALL4
- Protein
- p.Pro28=
- Coding
- c.84G>A
- MANE Select
- NM_020436
- Type
- single nucleotide variant
- Location
- chr20:51802325 (GRCh38)
- Gene constraint
- LOEUF 0.184 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 51.86 · 14 PDB
- Residue 28
- the 'disordered' region
Similar variants
- SALL4 p.Arg573Ter Pathogenic ★★ same type
- SALL4 p.Arg831Ter Pathogenic ★★ same type
- SALL4 p.Arg865Ter Pathogenic/Likely pathogenic ★★ same type
- SALL4 c.2743-3T>C Uncertain significance ★★ same type
- SALL4 p.Ala1004Val Uncertain significance ★★ ⚠ same type
- SALL4 p.Ala118Val Uncertain significance ★★ ⚠ same type
- SALL4 p.Ala149Val Uncertain significance ★★ ⚠ same type
- SALL4 p.Ala192Glu Uncertain significance ★★ ⚠ same type
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/sall4-p-pro28 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown