SALL4 p.Val477=
c.1431C>A · rs753427438 · VCV746468
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0117%, amr)
Conditions
1
Duane-radial ray 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 3.2 | GERP -3, phastCons 1 |
| Overall | ||
| CADD | 5.728 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0117%
Admixed American · 7/60,018 alleles
Filtering AF
0.00543%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0038%
Overall
0.000434%
7/1,614,154 alleles · ultra-rare
exomes 7/1,461,884 · genomes 0/152,270 · joint denominator
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.Val477=
- Coding
- c.1431C>A
- MANE Select
- NM_020436
- dbSNP
- rs753427438
- Type
- single nucleotide variant
- Location
- chr20:51791052 (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 condition
- SALL4 p.Arg831Ter Pathogenic ★★ same condition
- SALL4 p.Arg865Ter Pathogenic/Likely pathogenic ★★ same condition
- SALL4 c.2743-3T>C Uncertain significance ★★ same condition
- SALL4 p.Ala1004Val Uncertain significance ★★ ⚠ same condition
- SALL4 p.Ala118Val Uncertain significance ★★ ⚠ same condition
- SALL4 p.Ala149Val Uncertain significance ★★ ⚠ same condition
- SALL4 p.Ala192Glu 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/sall4-p-val477 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown