F5 p.Pro1863=
c.5589C>A · rs148772659 · VCV293579
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.185%, afr)
Conditions
5
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 | GERP 1.2, phastCons 1 |
| Overall | ||
| CADD | 7.622 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.185%
African / African-American · 139/74,982 alleles
Filtering AF
0.16%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.151%
Overall
0.00992%
160/1,613,456 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.185% | 539 |
| Admixed American | 0.02% | 4,994 |
| Middle Eastern | 0.0167% | 5,982 |
| Remaining individualsnot grpmax-eligible | 0.00961% | 10,408 |
| South Asian | 0.0022% | 45,531 |
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.Pro1863=
- Coding
- c.5589C>A
- MANE Select
- NM_000130
- dbSNP
- rs148772659
- Type
- single nucleotide variant
- Location
- chr1:169527925 (GRCh38)
- Gene constraint
- LOEUF 0.704 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 62.57 · 23 PDB
- Residue 1863
- a β-strand; the f5/8 type a 3 domain; the plastocyanin-like 6 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-pro1863 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown