CYBRD1 p.Pro148=
c.444G>A · rs202158377 · VCV3079297
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0802%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.03 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.92 | GERP -1.6 |
| Overall | ||
| CADD | 10.39 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0802%
South Asian · 73/91,062 alleles
Filtering AF
0.0654%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0599%
Overall
0.0135%
218/1,613,532 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0802% | 1,247 |
| African / African-American | 0.0667% | 1,500 |
| European (non-Finnish) | 0.00746% | 13,406 |
| East Asian | 0.00669% | 14,947 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,821 |
| Finnishnot grpmax-eligible | 0.00156% | 63,958 |
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.Pro148=
- Coding
- c.444G>A
- MANE Select
- NM_024843
- dbSNP
- rs202158377
- Type
- single nucleotide variant
- Location
- chr2:171553387 (GRCh38)
- Gene constraint
- LOEUF 0.941 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.19 · 2 PDB
- Residue 148
- the cytochrome b561 domain
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-pro148 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown