SH3BP2 p.Pro202=
c.606G>A · rs775926639 · VCV1167113
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0567%, amr)
Conditions
1
cherubism
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 -6.1 | GERP -2.9 |
| Overall | ||
| CADD | 3.234 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0567%
Admixed American · 34/59,984 alleles
Filtering AF
0.0416%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0365%
Overall
0.00298%
48/1,613,434 alleles · ultra-rare
exomes 44/1,461,412 · genomes 4/152,022 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0567% | 1,764 |
| African / African-American | 0.00267% | 37,432 |
| South Asian | 0.0011% | 91,080 |
| European (non-Finnish) | 0.000932% | 107,270 |
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
- SH3BP2
- Protein
- p.Pro202=
- Coding
- c.606G>A
- MANE Select
- NM_001122681
- dbSNP
- rs775926639
- Type
- single nucleotide variant
- Location
- chr4:2829512 (GRCh38)
- Gene constraint
- LOEUF 0.958 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 66.04 · 2 PDB
- Residue 202
- the 'disordered' region
Similar variants
- SH3BP2 p.Pro202Leu Uncertain significance ★★ ⚠ same residue
- SH3BP2 p.Pro202Ser Uncertain significance ★ same residue
- SH3BP2 p.Arg415Gln Pathogenic ★★ ⚠ same condition
- SH3BP2 p.Gly420Arg Pathogenic ★★ ⚠ same condition
- SH3BP2 p.Pro418Arg Pathogenic ★★ ⚠ same condition
- SH3BP2 p.Pro418His Pathogenic/Likely pathogenic ★★ ⚠ same condition
- SH3BP2 p.Pro418Leu Pathogenic/Likely pathogenic ★★ ⚠ same condition
- SH3BP2 p.Pro418Thr Pathogenic/Likely pathogenic ★★ ⚠ same condition
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/sh3bp2-p-pro202 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown