F2 p.Pro233=
c.699C>T · rs1156387909 · VCV1756516
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000508%, nfe)
Conditions
1
Inborn genetic diseases
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 -0.89 | GERP -2.9 |
| Overall | ||
| CADD | 4.938 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000508%
European (non-Finnish) · 6/1,179,980 alleles
Filtering AF
0.000183%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00012%
Overall
0.000372%
6/1,614,000 alleles · very rare
exomes 6/1,461,648 · genomes 0/152,352 · joint denominator
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
- F2
- Protein
- p.Pro233=
- Coding
- c.699C>T
- MANE Select
- NM_000506
- dbSNP
- rs1156387909
- Type
- single nucleotide variant
- Location
- chr11:46725998 (GRCh38)
- Gene constraint
- LOEUF 0.552 · pLI 0.15 (gnomAD)
- Structure
- AlphaFold pLDDT 84.37 · 480 PDB
- Residue 233
- the kringle 2 domain
Similar variants
- F2 p.Ala490Thr Uncertain significance ★★ ⚠ same condition
- F2 p.Arg217Gln Uncertain significance ★★ ⚠ same condition
- F2 p.Arg224Cys Uncertain significance ★★ ⚠ same condition
- F2 p.Arg35Trp Uncertain significance ★★ ⚠ same condition
- F2 p.Ile438Thr Uncertain significance ★★ ⚠ same condition
- F2 p.Pro471Thr Uncertain significance ★★ ⚠ same condition
- F2 p.Thr488Met Uncertain significance ★★ ⚠ same condition
- F2 p.Val258Leu 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/f2-p-pro233 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown