SALL4 p.Pro204=
c.612C>T · VCV4945394
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.01%, amr)
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 -4.7 |
| Overall | ||
| CADD | 0.998 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.01%
Admixed American · 6/60,030 alleles
Filtering AF
0.00428%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00295%
Overall
0.00297%
48/1,614,078 alleles · very rare
exomes 47/1,461,710 · genomes 1/152,368 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.01% | 10,005 |
| East Asian | 0.00446% | 22,441 |
| African / African-American | 0.004% | 25,025 |
| European (non-Finnish) | 0.00297% | 33,714 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,512 |
| South Asian | 0.0011% | 91,074 |
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.Pro204=
- Coding
- c.612C>T
- MANE Select
- NM_020436
- Type
- single nucleotide variant
- Location
- chr20:51791871 (GRCh38)
- Gene constraint
- LOEUF 0.184 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 51.86 · 14 PDB
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-pro204 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown