SALL1 p.Ser462=
c.1386T>C · VCV4929911
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00133%, afr)
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 2.3 | GERP -0.41, phastCons 1 |
| Overall | ||
| CADD | 9.108 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00133%
African / African-American · 1/74,952 alleles
Filtering AF
0.000124%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 9e-05%
Overall
0.000372%
6/1,614,126 alleles · very rare
exomes 5/1,461,894 · genomes 1/152,232 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00133% | 74,952 |
| European (non-Finnish) | 0.000424% | 236,009 |
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.Ser462=
- Coding
- c.1386T>C
- MANE Select
- NM_002968
- Type
- single nucleotide variant
- Location
- chr16:51140836 (GRCh38)
- Gene constraint
- LOEUF 0.228 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 49.54
Similar variants
- SALL1 p.Ser462fs Pathogenic same residue
- SALL1 p.Arg1054Ter Pathogenic/Likely pathogenic ★★ same type
- SALL1 p.Arg276Ter Pathogenic/Likely pathogenic ★★ same type
- SALL1 p.Arg786Ter Pathogenic ★★ same type
- SALL1 p.Gln201Ter Pathogenic/Likely pathogenic ★★ same type
- SALL1 p.Gln237Ter Pathogenic/Likely pathogenic ★★ same type
- SALL1 p.Gln243Ter Pathogenic ★★ same type
- SALL1 p.Gln272Ter Pathogenic ★★ 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/sall1-p-ser462 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown