CYBRD1 p.Pro222=
c.666G>A · rs150461979 · VCV3079299
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0164%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.06 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1.8 | GERP -3 |
| Overall | ||
| CADD | 7.495 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0164%
Middle Eastern · 1/6,084 alleles
Filtering AF
0.00528%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00462%
Overall
0.00527%
85/1,613,856 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0164% | 6,084 |
| African / African-American | 0.0107% | 9,362 |
| European (non-Finnish) | 0.00619% | 16,164 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,825 |
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
- CYBRD1
- Protein
- p.Pro222=
- Coding
- c.666G>A
- MANE Select
- NM_024843
- dbSNP
- rs150461979
- Type
- single nucleotide variant
- Location
- chr2:171554632 (GRCh38)
- Gene constraint
- LOEUF 0.941 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.19 · 2 PDB
- Residue 222
- an α-helix
Similar variants
- CYBRD1 p.Ser266Asn Benign ★★ same type
- CYBRD1 c.19+1G>T Uncertain significance ★ same type
- CYBRD1 p.Ala114Val Uncertain significance ★ ⚠ same type
- CYBRD1 p.Ala213Asp Uncertain significance ★ ⚠ same type
- CYBRD1 p.Ala93Val Uncertain significance ★ same type
- CYBRD1 p.Arg273Lys Uncertain significance ★ ⚠ same type
- CYBRD1 p.Arg283Lys Uncertain significance ★ ⚠ same type
- CYBRD1 p.Arg35Gly 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/cybrd1-p-pro222 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown