C5 p.Lys1602=
c.4806A>G · rs41258306 · VCV402450
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Common
common (popmax 6.86%, nfe) — too common for a highly-penetrant pathogenic allele
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 0.016 | GERP -4.3, phastCons 0.014 |
| Overall | ||
| CADD | 2.047 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
6.86%
European (non-Finnish) · 80,876/1,179,136 alleles
Filtering AF
6.82%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 6.8%
Overall
6.37%
102,715/1,613,206 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 6.86% | 15 |
| South Asian | 6.81% | 15 |
| Middle Eastern | 6.45% | 15 |
| African / African-American | 6.4% | 16 |
| Remaining individualsnot grpmax-eligible | 6.33% | 16 |
| Ashkenazi Jewishnot grpmax-eligible | 6.21% | 16 |
| Admixed American | 5.92% | 17 |
| Amishnot grpmax-eligible | 3.07% | 33 |
| Finnishnot grpmax-eligible | 1.62% | 62 |
| East Asian | 0.0936% | 1,069 |
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
- C5
- Protein
- p.Lys1602=
- Coding
- c.4806A>G
- MANE Select
- NM_001735
- dbSNP
- rs41258306
- Type
- single nucleotide variant
- Location
- chr9:120953825 (GRCh38)
- Gene constraint
- LOEUF 0.779 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.67 · 49 PDB
- Residue 1602
- a β-strand; a disulfide bond; a UniProt-annotated variant site (in c5d); the ntr domain
Similar variants
- C5 c.2257+1G>A Likely pathogenic ★★ same type
- C5 c.4679-2A>G Likely pathogenic ★★ same type
- C5 p.Arg1476Ter Pathogenic/Likely pathogenic ★★ same type
- C5 p.Gln19Ter Pathogenic ★★ same type
- C5 p.Glu1437Ter Pathogenic/Likely pathogenic ★★ same type
- C5 p.Trp469Ter Pathogenic/Likely pathogenic ★★ same type
- C5 c.2059+3A>G Uncertain significance ★★ same type
- C5 c.3391-13T>A 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/c5-p-lys1602 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown