Is CFB p.Pro369Leu (c.1106C>T) pathogenic?

CFB p.Pro369Leu (c.1106C>T) is classified Likely benign in CFB (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-01-06). AlphaMissense: likely benign (0.1297); Rare (popmax 0.308%, sas); Associated with atypical hemolytic-uremic syndrome.

What condition is associated with CFB p.Pro369Leu (c.1106C>T)?

CFB p.Pro369Leu (c.1106C>T) is associated with atypical hemolytic-uremic syndrome (ClinVar).

How common is CFB p.Pro369Leu (c.1106C>T) in the general population?

CFB p.Pro369Leu (c.1106C>T) is rare (popmax 0.308%, sas) (gnomAD).

How is Atypical hemolytic uremic syndrome inherited?

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

What do computational predictors say about CFB p.Pro369Leu (c.1106C>T)?

AlphaMissense predicts likely benign (score 0.1297) — an in-silico prediction, not a clinical call.

CFB p.Pro369Leu

c.1106C>T · rs200890358 · VCV1531488

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1297 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.308%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

atypical hemolytic-uremic syndrome

Computational evidence

Protein change
AlphaMissense	0.1297	likely benign
REVEL	0.19	benign-leaning
SaProt	LLR -8.40	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.39	GERP -3.8
Overall
CADD	5.99	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 0.308% South Asian · 280/91,052 alleles

Filtering AF 0.278% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.266%

Overall 0.02% 323/1,612,858 alleles · rare exomes 300/1,460,754 · genomes 23/152,104 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.308%	325
Middle Eastern	0.0331%	3,024
Remaining individualsnot grpmax-eligible	0.0224%	4,464
East Asian	0.00446%	22,440
African / African-American	0.00267%	37,478
European (non-Finnish)	0.00195%	51,304

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: CFB
Protein: p.Pro369Leu
Coding: c.1106C>T
MANE Select: NM_001710
dbSNP: rs200890358
Type: single nucleotide variant
Location: chr6:31948899 (GRCh38)
Gene constraint: LOEUF 0.719 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.54 · 28 PDB
Residue 369: a β-strand; the vwfa domain

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

Disease context

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

For Atypical hemolytic uremic syndrome (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive, Not applicable
Onset: All ages
Prevalence: 1-9 / 1 000 000 (United States)

Similar variants

CFB p.Pro369Ala Uncertain significance ★★ ⚠ same residue
CFB p.Arg138Gln Uncertain significance ★★ ⚠ same condition
CFB p.Arg138Trp Uncertain significance ★★ ⚠ same condition
CFB p.Arg203Gln Uncertain significance ★★ same condition
CFB p.Arg379Cys Uncertain significance ★★ same condition
CFB p.Gln256Ter Uncertain significance ★★ same condition
CFB p.Glu601Lys Uncertain significance ★★ ⚠ same condition
CFB p.Ser284Asn Uncertain significance ★★ ⚠ 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/cfb-p-pro369leu (accessed [today's date]).

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