CFD p.Thr190=
c.570C>T · rs372792553 · VCV715886
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.57%, 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 -2.7 | GERP -3.7 |
| Overall | ||
| CADD | 1.12 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.57%
Middle Eastern · 34/5,966 alleles
Filtering AF
0.454%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.439%
Overall
0.0732%
1,153/1,574,138 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.57% | 175 |
| South Asian | 0.492% | 203 |
| Admixed American | 0.145% | 689 |
| Remaining individualsnot grpmax-eligible | 0.088% | 1,136 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0483% | 2,071 |
| European (non-Finnish) | 0.0447% | 2,236 |
| African / African-American | 0.0188% | 5,318 |
| East Asian | 0.0023% | 43,388 |
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.Thr190=
- Coding
- c.570C>T
- MANE Select
- NM_001928
- dbSNP
- rs372792553
- Type
- single nucleotide variant
- Location
- chr19:861911 (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 190
- a disulfide bond; the peptidase s1 domain
Similar variants
- CFD p.Thr190Ile Uncertain significance ★ ⚠ same residue
- 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
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-thr190 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown