SOBP p.Pro500=
c.1500G>T · rs372926482 · VCV758864
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0331%, mid)
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 -0.011 | GERP -0.91, phastCons 0.45 |
| Overall | ||
| CADD | 7.441 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0331%
Middle Eastern · 2/6,036 alleles
Filtering AF
0.00584%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00354%
Overall
0.00409%
65/1,589,438 alleles · ultra-rare
exomes 62/1,437,456 · genomes 3/151,982 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0331% | 3,018 |
| European (non-Finnish) | 0.00494% | 20,257 |
| Remaining individualsnot grpmax-eligible | 0.00485% | 20,633 |
| Admixed American | 0.0034% | 29,441 |
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.Pro500=
- Coding
- c.1500G>T
- MANE Select
- NM_018013
- dbSNP
- rs372926482
- Type
- single nucleotide variant
- Location
- chr6:107634344 (GRCh38)
- Gene constraint
- LOEUF 0.191 · pLI 1.00 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 52.41
Similar variants
- 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
- SOBP p.Pro441Ser 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-pro500 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown