Is C3 p.Arg425Cys (c.1273C>T) pathogenic?

C3 p.Arg425Cys (c.1273C>T) is classified Conflicting classifications of pathogenicity in C3 (ClinVar, Conflicting submitters, 7 submitters; last evaluated 2026-09-17). AlphaMissense: likely benign (0.248); Rare (popmax 0.205%, eas); Associated with atypical hemolytic-uremic syndrome with C3 anomaly.

What condition is associated with C3 p.Arg425Cys (c.1273C>T)?

C3 p.Arg425Cys (c.1273C>T) is associated with atypical hemolytic-uremic syndrome with C3 anomaly, age related macular degeneration 9, complement component 3 deficiency (ClinVar).

How common is C3 p.Arg425Cys (c.1273C>T) in the general population?

C3 p.Arg425Cys (c.1273C>T) is rare (popmax 0.205%, eas) (gnomAD).

What do computational predictors say about C3 p.Arg425Cys (c.1273C>T)?

AlphaMissense predicts likely benign (score 0.248) — an in-silico prediction, not a clinical call.

C3 p.Arg425Cys

c.1273C>T · rs200967589 · VCV449567

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 7 submitters

AlphaMissense

likely benign

0.248 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.205%, eas)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

atypical hemolytic-uremic syndrome with C3 anomaly

Computational evidence

Protein change
AlphaMissense	0.248	likely benign
REVEL	0.157	moderately benign-leaning
SaProt	LLR -10.41	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 3.2	GERP -0.74, phastCons 0.4
Regional constraint	o/e 0.74	unconstrained · MANE · 35 kb · p 3.5e-28 · regional, not allelic
Overall
CADD	21.8	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.205% East Asian · 92/44,880 alleles

Filtering AF 0.171% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.158%

Overall 0.00893% 144/1,611,836 alleles · rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.205%	488
Finnishnot grpmax-eligible	0.0129%	7,749
Remaining individualsnot grpmax-eligible	0.008%	12,496
European (non-Finnish)	0.00314%	31,888
Admixed American	0.00167%	60,006
African / African-American	0.00133%	74,994

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: C3
Protein: p.Arg425Cys
Coding: c.1273C>T
MANE Select: NM_000064
dbSNP: rs200967589
Type: single nucleotide variant
Location: chr19:6711193 (GRCh38)
Gene constraint: LOEUF 0.541 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 79.84 · 80 PDB
Residue 425: a β-strand

Full C3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

atypical hemolytic-uremic syndrome with C3 anomaly — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: age related macular degeneration 9 complement component 3 deficiency C3 glomerulonephritis atypical hemolytic-uremic syndrome

Similar variants

C3 p.Arg425Leu Uncertain significance ★★ ⚠ same residue
C3 p.Arg425His Uncertain significance ★ ⚠ same residue
C3 c.1003+1G>A Pathogenic/Likely pathogenic ★★ same condition
C3 c.2863+1G>T Likely pathogenic ★★ same condition
C3 c.4030-2A>G Likely pathogenic ★★ same condition
C3 p.Arg161Trp Pathogenic/Likely pathogenic ★★ ⚠ same condition
C3 p.Arg592Gln Pathogenic/Likely pathogenic ★★ ⚠ same condition
C3 p.Arg592Trp Likely 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/c3-p-arg425cys (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown