CFI p.Asp242=
c.726T>C · rs144048103 · VCV2149828
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00017%, nfe)
Conditions
1
CFI-related disorder
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 · A>T here scores Δ0.27 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.89 | GERP -3.3 |
| Overall | ||
| CADD | 0.74 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00017%
European (non-Finnish) · 2/1,177,788 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000124%
2/1,611,558 alleles · very rare
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.Asp242=
- Coding
- c.726T>C
- MANE Select
- NM_000204
- dbSNP
- rs144048103
- Type
- single nucleotide variant
- Location
- chr4:109760569 (GRCh38)
- Gene constraint
- LOEUF 1.076 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.50 · 2 PDB
- Residue 242
- a binding site; a disulfide bond; the ldl-receptor class a 1 domain; a β-strand
Similar variants
- CFI p.Asp242Ala Uncertain significance ★ same residue
- CFI p.Arg187Ter Pathogenic/Likely pathogenic ★★ same condition
- CFI p.Arg474Ter Pathogenic/Likely pathogenic ★★ same condition
- CFI p.Trp145Ter Pathogenic ★★ same condition
- CFI p.Ala153Thr Uncertain significance ★★ ⚠ same condition
- CFI p.Ala76Gly Uncertain significance ★★ ⚠ same condition
- CFI p.Arg317Gln Uncertain significance ★★ ⚠ same condition
- CFI p.Arg502Cys Uncertain significance ★★ ⚠ 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/cfi-p-asp242 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown