SOBP p.Ala752=
c.2256G>A · rs546746716 · VCV760607
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0404%, afr)
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 0.56 | GERP 0.18, phastCons 0.97 |
| Overall | ||
| CADD | 10.58 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0404%
African / African-American · 30/74,302 alleles
Filtering AF
0.029%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0251%
Overall
0.00219%
35/1,600,148 alleles · ultra-rare
exomes 10/1,448,422 · genomes 25/151,726 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0404% | 2,477 |
| Remaining individualsnot grpmax-eligible | 0.00486% | 20,584 |
| Admixed American | 0.00171% | 58,636 |
| European (non-Finnish) | 8.52e-05% | 1,173,592 |
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
- SOBP
- Protein
- p.Ala752=
- Coding
- c.2256G>A
- MANE Select
- NM_018013
- dbSNP
- rs546746716
- Type
- single nucleotide variant
- Location
- chr6:107635100 (GRCh38)
- Gene constraint
- LOEUF 0.191 · pLI 1.00 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 52.41
- Residue 752
- the 'disordered' region
Similar variants
- SOBP p.Ala752Val Uncertain significance ★ ⚠ same residue
- SOBP c.573+12G>A Uncertain significance ★★ same type
- SOBP p.Ala208Thr Uncertain significance ★★ ⚠ same type
- SOBP p.Ala702Val Uncertain significance ★★ ⚠ same type
- SOBP p.Glu89Lys Uncertain significance ★★ ⚠ same type
- SOBP p.Lys862Asn Uncertain significance ★★ ⚠ same type
- SOBP p.Pro138Leu Uncertain significance ★★ same type
- SOBP p.Pro139Ser 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/sobp-p-ala752 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown