SOBP p.Pro473=
c.1419A>C · rs1226628501 · VCV2656817
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00212%, 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 -0.91 | GERP -2.1 |
| Overall | ||
| CADD | 6.213 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00212%
African / African-American · 1/47,248 alleles
Filtering AF
0.000143%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000104%
Overall
0.00046%
6/1,304,752 alleles · very rare
exomes 1/1,233,540 · genomes 5/71,212 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00212% | 47,248 |
| European (non-Finnish) | 0.000489% | 204,571 |
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.Pro473=
- Coding
- c.1419A>C
- MANE Select
- NM_018013
- dbSNP
- rs1226628501
- Type
- single nucleotide variant
- Location
- chr6:107634263 (GRCh38)
- Gene constraint
- LOEUF 0.191 · pLI 1.00 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 52.41
- Residue 473
- the 'disordered' region
Similar variants
- SOBP p.Pro473Leu 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-pro473 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown