CFP p.Pro204=
c.612C>T · rs1031008836 · VCV2716648
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00101%, nfe)
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 0.53 | GERP -0.51, phastCons 0.99 |
| Overall | ||
| CADD | 3.136 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00101%
European (non-Finnish) · 9/890,157 alleles
Filtering AF
0.000476%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000345%
Overall
0.000749%
9/1,202,145 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
- CFP
- Protein
- p.Pro204=
- Coding
- c.612C>T
- MANE Select
- NM_001145252
- dbSNP
- rs1031008836
- Type
- single nucleotide variant
- Location
- chrX:47627295 (GRCh38)
- Structure
- AlphaFold pLDDT 83.75 · 14 PDB
- Residue 204
- the tsp type-1 3 domain; a UniProt-annotated variant site (in); an α-helix
Similar variants
- CFP p.Pro204Arg Uncertain significance ★★ ⚠ same residue
- CFP p.Pro204Leu Benign/Likely benign ★★ 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
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-pro204 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown