CFD p.Arg240=
c.720C>T · rs370962604 · VCV1576069
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0501%, mid)
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 -3.8 | GERP -4.9 |
| Overall | ||
| CADD | 7.812 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0501%
Middle Eastern · 3/5,990 alleles
Filtering AF
0.0157%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0131%
Overall
0.00182%
28/1,540,238 alleles · ultra-rare
exomes 26/1,387,938 · genomes 2/152,300 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0501% | 1,997 |
| African / African-American | 0.0245% | 4,088 |
| Remaining individualsnot grpmax-eligible | 0.00831% | 12,036 |
| Admixed American | 0.00196% | 51,124 |
| South Asian | 0.00119% | 84,278 |
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
- CFD
- Protein
- p.Arg240=
- Coding
- c.720C>T
- MANE Select
- NM_001928
- dbSNP
- rs370962604
- Type
- single nucleotide variant
- Location
- chr19:863196 (GRCh38)
- Gene constraint
- LOEUF 1.948 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 91.19 · 40 PDB
- Residue 240
- the peptidase s1 domain; a β-strand
Similar variants
- CFD c.212+2T>G Likely pathogenic ★★ same type
- CFD c.56-1G>C Likely pathogenic ★★ same type
- CFD p.Tyr95Ter Pathogenic ★★ same type
- ELANE p.Gly203Arg Pathogenic ★★ same type
- ELANE p.Ser126Leu Pathogenic ★★ ⚠ same type
- CFD p.Ala100Pro Uncertain significance ★★ same type
- CFD p.Ala129Thr Uncertain significance ★★ ⚠ same type
- CFD p.Ala143Val 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/cfd-p-arg240 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown