CFP p.Ser90=
c.270G>A · rs146840844 · VCV2715750
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0457%, 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 -5.1 | GERP -3.5 |
| Overall | ||
| CADD | 0.11 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0457%
Middle Eastern · 2/4,377 alleles
Filtering AF
0.0095%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00728%
Overall
0.0024%
29/1,208,861 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0457% | 2,188 |
| South Asian | 0.0177% | 5,662 |
| African / African-American | 0.0175% | 5,702 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00455% | 21,992 |
| Remaining individualsnot grpmax-eligible | 0.0021% | 47,550 |
| European (non-Finnish) | 0.000559% | 178,940 |
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
- CFP
- Protein
- p.Ser90=
- Coding
- c.270G>A
- MANE Select
- NM_001145252
- dbSNP
- rs146840844
- Type
- single nucleotide variant
- Location
- chrX:47628235 (GRCh38)
- Structure
- AlphaFold pLDDT 83.75 · 14 PDB
- Residue 90
- the tsp type-1 1 domain; a β-strand
Similar variants
- CFP p.Ser90Leu Uncertain significance ★★ same residue
- CFP p.Trp321Gly Pathogenic ★★ same type
- CFP p.Ala402Gly Uncertain significance ★★ ⚠ same type
- CFP p.Arg157Gln Uncertain significance ★★ ⚠ same type
- CFP p.Arg157Trp Uncertain significance ★★ ⚠ same type
- CFP p.Arg159Cys Uncertain significance ★★ ⚠ same type
- CFP p.Arg247Trp Uncertain significance ★★ ⚠ same type
- CFP p.Arg438Trp 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/cfp-p-ser90 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown