CFHR3 p.Arg320=
c.958C>A · rs145280059 · VCV734286
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.959%, 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 -13 | GERP -2.7 |
| Overall | ||
| CADD | 1.219 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.959%
Middle Eastern · 51/5,316 alleles
Filtering AF
0.75%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.675%
Overall
0.0502%
766/1,525,872 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.959% | 104 |
| Ashkenazi Jewishnot grpmax-eligible | 0.658% | 152 |
| African / African-American | 0.285% | 351 |
| South Asian | 0.118% | 845 |
| Admixed American | 0.0931% | 1,074 |
| Remaining individualsnot grpmax-eligible | 0.0764% | 1,309 |
| European (non-Finnish) | 0.015% | 6,679 |
| Finnishnot grpmax-eligible | 0.00162% | 61,806 |
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
- CFHR3
- Protein
- p.Arg320=
- Coding
- c.958C>A
- MANE Select
- NM_021023
- dbSNP
- rs145280059
- Type
- single nucleotide variant
- Location
- chr1:196793478 (GRCh38)
- Gene constraint
- LOEUF 1.302 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 91.93
- Residue 320
- a disulfide bond; the sushi 5 domain
Similar variants
- CFHR3 p.Arg320Gln Uncertain significance ★★ ⚠ same residue
- CFHR3 p.Arg320Trp Uncertain significance ★ ⚠ same residue
- CFHR3 c.796+1G>A Uncertain significance ★★ same type
- CFHR3 p.Gly119Ala Uncertain significance ★★ ⚠ same type
- CFHR3 p.Ile70Thr Uncertain significance ★★ ⚠ same type
- CFHR3 p.Tyr118Ter Uncertain significance ★★ same type
- CFHR3 c.431-88C>T Benign ★★ same type
- CFHR3 c.58+8A>G Likely benign ★★ 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/cfhr3-p-arg320 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown