F5 p.Thr206=
c.618G>A · rs149072504 · VCV2561206
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0318%, sas)
Conditions
2
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 3.2 | GERP 0.45, phastCons 1 |
| Overall | ||
| CADD | 11.72 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0318%
South Asian · 29/91,086 alleles
Filtering AF
0.0228%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0196%
Overall
0.00335%
54/1,613,814 alleles · ultra-rare
exomes 45/1,461,548 · genomes 9/152,266 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0318% | 3,141 |
| Remaining individualsnot grpmax-eligible | 0.0096% | 10,415 |
| East Asian | 0.00669% | 14,955 |
| Admixed American | 0.00333% | 29,997 |
| European (non-Finnish) | 0.00119% | 84,272 |
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
- F5
- Protein
- p.Thr206=
- Coding
- c.618G>A
- MANE Select
- NM_000130
- dbSNP
- rs149072504
- Type
- single nucleotide variant
- Location
- chr1:169559265 (GRCh38)
- Gene constraint
- LOEUF 0.704 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 62.57 · 23 PDB
- Residue 206
- a β-strand; the f5/8 type a 1 domain; the plastocyanin-like 2 domain
Similar variants
- F5 c.1297-2A>G Pathogenic/Likely pathogenic ★★ same condition
- F5 p.Arg1030Ter Pathogenic ★★ same condition
- F5 p.Arg146Ter Pathogenic/Likely pathogenic ★★ same condition
- F5 p.Arg1621Ter Pathogenic/Likely pathogenic ★★ same condition
- F5 p.Arg1634Ter Pathogenic/Likely pathogenic ★★ same condition
- F5 p.Arg2102His Pathogenic/Likely pathogenic ★★ same condition
- F5 p.Arg740Ter Pathogenic/Likely pathogenic ★★ same condition
- F5 p.Asp96His Pathogenic ★★ 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/f5-p-thr206 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown