CFI p.Gly232=
c.696G>A · rs144145014 · VCV2415833
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0201%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.29 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.35 | GERP -0.18, phastCons 0.083 |
| Overall | ||
| CADD | 6.071 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0201%
East Asian · 9/44,830 alleles
Filtering AF
0.0104%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0078%
Overall
0.00603%
97/1,609,292 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0201% | 4,981 |
| Middle Eastern | 0.0165% | 6,058 |
| European (non-Finnish) | 0.00706% | 14,165 |
| Remaining individualsnot grpmax-eligible | 0.00481% | 20,773 |
| Admixed American | 0.00167% | 60,008 |
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
- CFI
- Protein
- p.Gly232=
- Coding
- c.696G>A
- MANE Select
- NM_000204
- dbSNP
- rs144145014
- Type
- single nucleotide variant
- Location
- chr4:109760599 (GRCh38)
- Gene constraint
- LOEUF 1.076 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.50 · 2 PDB
- Residue 232
- a disulfide bond; the ldl-receptor class a 1 domain
Similar variants
- CFI c.1429+1G>C Pathogenic/Likely pathogenic ★★ same type
- CFI c.57+1G>C Likely pathogenic ★★ same type
- CFI c.658+1G>A Likely pathogenic ★★ same type
- CFI c.905-1G>C Likely pathogenic ★★ same type
- CFI p.Ala258Thr Pathogenic/Likely pathogenic ★★ ⚠ same type
- CFI p.Arg187Ter Pathogenic/Likely pathogenic ★★ same type
- CFI p.Arg474Ter Pathogenic/Likely pathogenic ★★ same type
- CFI p.His380Arg Pathogenic/Likely pathogenic ★★ 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/cfi-p-gly232 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown