Is CFAP52 p.Arg369Gln (c.1106G>A) pathogenic?

CFAP52 p.Arg369Gln (c.1106G>A) is classified Conflicting classifications of pathogenicity in CFAP52 (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2025-06-17). AlphaMissense: likely benign (0.3071); Rare (popmax 0.197%, nfe); Associated with situs inversus.

What condition is associated with CFAP52 p.Arg369Gln (c.1106G>A)?

CFAP52 p.Arg369Gln (c.1106G>A) is associated with situs inversus (ClinVar).

How common is CFAP52 p.Arg369Gln (c.1106G>A) in the general population?

CFAP52 p.Arg369Gln (c.1106G>A) is rare (popmax 0.197%, nfe) (gnomAD).

What do computational predictors say about CFAP52 p.Arg369Gln (c.1106G>A)?

AlphaMissense predicts likely benign (score 0.3071) — an in-silico prediction, not a clinical call.

CFAP52 p.Arg369Gln

c.1106G>A · rs141646758 · VCV1038824

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.3071 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.197%, nfe)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

situs inversus

Computational evidence

Protein change
AlphaMissense	0.3071	likely benign
REVEL	0.608	indeterminate
SaProt	LLR -14.25	damaging
⇒ SaProt calls this damaging; AlphaMissense does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 1.8, phastCons 1
Regional constraint	o/e 1.00	unconstrained · MANE · 66 kb · p 0.9 · regional, not allelic
Overall
CADD	32.0	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 0.197% European (non-Finnish) · 2,330/1,180,020 alleles

Filtering AF 0.191% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.188%

Overall 0.152% 2,456/1,614,104 alleles · rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.197%	506
Remaining individualsnot grpmax-eligible	0.0752%	1,330
Finnishnot grpmax-eligible	0.0344%	2,910
African / African-American	0.028%	3,573
South Asian	0.0264%	3,795
Admixed American	0.015%	6,666
East Asian	0.00669%	14,959

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: CFAP52
Protein: p.Arg369Gln
Coding: c.1106G>A
MANE Select: NM_145054
dbSNP: rs141646758
Type: single nucleotide variant
Location: chr17:9628752 (GRCh38)
Gene constraint: LOEUF 1.022 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 93.59 · 2 PDB

Full CFAP52 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

situs inversus — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CFAP52 p.Arg369Trp Uncertain significance ★ ⚠ same residue
CFAP52 p.Ala147Thr Uncertain significance ★★ ⚠ same condition
CFAP52 p.Ala161Asp Uncertain significance ★★ ⚠ same condition
CFAP52 p.Arg170Gln Uncertain significance ★★ ⚠ same condition
CFAP52 p.Arg594Cys Uncertain significance ★★ ⚠ same condition
CFAP52 p.Gly343Ser Uncertain significance ★★ ⚠ same condition
CFAP52 p.Gly534Ala Uncertain significance ★★ same condition
CFAP52 p.Met551Thr 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/cfap52-p-arg369gln (accessed [today's date]).

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