Is C3 p.Thr612= (c.1836G>A) pathogenic?

C3 p.Thr612= (c.1836G>A) is classified Benign/Likely benign in C3 (ClinVar, Multiple submitters, 8 submitters; last evaluated 2026-02-04). Common (popmax 41.9%, eas) — too common for a highly-penetrant pathogenic allele; Associated with complement component 3 deficiency.

What condition is associated with C3 p.Thr612= (c.1836G>A)?

C3 p.Thr612= (c.1836G>A) is associated with complement component 3 deficiency, age related macular degeneration 9, atypical hemolytic-uremic syndrome with C3 anomaly (ClinVar).

How is Complement component 3 deficiency inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

C3 p.Thr612=

Q: How common is C3 p.Thr612= (c.1836G>A) in the general population?

C3 p.Thr612= (c.1836G>A) is common (popmax 41.9%, eas) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.1836G>A · rs2230205 · VCV330317

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 8 submitters

gnomAD v4.1

Common

common (popmax 41.9%, eas) — too common for a highly-penetrant pathogenic allele

Conditions

complement component 3 deficiency

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 -2	GERP -3.4
Overall
CADD	3.437	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 41.9% East Asian · 18,770/44,744 alleles

Filtering AF 41.4% ClinGen BA1/BS1 input FAF95, joint · FAF99 41.2%

Overall 14.5% 233,564/1,612,072 alleles · common

Ancestry group	Frequency	1 in
East Asiangrpmax	41.9%	2
South Asian	22.6%	4
Ashkenazi Jewishnot grpmax-eligible	19.9%	5
Finnishnot grpmax-eligible	19.7%	5
Amishnot grpmax-eligible	19.1%	5
Remaining individualsnot grpmax-eligible	15.7%	6
Middle Eastern	13.1%	8
European (non-Finnish)	12.6%	8
African / African-American	12.1%	8
Admixed American	11.7%	9

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.Thr612=
Coding: c.1836G>A
MANE Select: NM_000064
dbSNP: rs2230205
Type: single nucleotide variant
Location: chr19:6709693 (GRCh38)
Gene constraint: LOEUF 0.541 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 79.84 · 80 PDB
Residue 612: a disulfide bond

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

Disease context

complement component 3 deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: age related macular degeneration 9 atypical hemolytic-uremic syndrome with C3 anomaly

For Complement component 3 deficiency (Orphanet):

Inheritance: Autosomal recessive
Onset: Childhood

Similar variants

C3 p.Thr612Met 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
C3 p.Arg764Ter Pathogenic/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-thr612 (accessed [today's date]).

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