SOBP p.Pro463=
c.1389G>C · rs377021315 · VCV3067282
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.822%, amr)
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 -1.6 | GERP -2.8 |
| Overall | ||
| CADD | 2.559 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.822%
Admixed American · 290/35,290 alleles
Filtering AF
0.744%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.714%
Overall
0.0745%
971/1,303,376 alleles · rare
exomes 962/1,218,552 · genomes 9/84,824 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.822% | 122 |
| South Asian | 0.442% | 226 |
| East Asian | 0.221% | 453 |
| Ashkenazi Jewishnot grpmax-eligible | 0.114% | 874 |
| Middle Eastern | 0.0987% | 1,013 |
| Finnishnot grpmax-eligible | 0.0967% | 1,034 |
| Remaining individualsnot grpmax-eligible | 0.0948% | 1,054 |
| African / African-American | 0.0444% | 2,252 |
| European (non-Finnish) | 0.0253% | 3,946 |
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.Pro463=
- Coding
- c.1389G>C
- MANE Select
- NM_018013
- dbSNP
- rs377021315
- Type
- single nucleotide variant
- Location
- chr6:107634233 (GRCh38)
- Gene constraint
- LOEUF 0.191 · pLI 1.00 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 52.41
- Residue 463
- the 'disordered' region
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-pro463 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown