Is CFAP52 p.Ala349= (c.1047A>T) pathogenic?

CFAP52 p.Ala349= (c.1047A>T) is classified Benign in CFAP52 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-08-10). Rare (popmax 0.384%, afr); Associated with situs inversus.

What condition is associated with CFAP52 p.Ala349= (c.1047A>T)?

CFAP52 p.Ala349= (c.1047A>T) is associated with situs inversus (ClinVar).

How common is CFAP52 p.Ala349= (c.1047A>T) in the general population?

CFAP52 p.Ala349= (c.1047A>T) is rare (popmax 0.384%, afr) (gnomAD).

CFAP52 p.Ala349=

c.1047A>T · rs113576151 · VCV766856

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

rare (popmax 0.384%, afr)

Conditions

situs inversus

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 -0.98	GERP -1.3, phastCons 0.001
Overall
CADD	7.792	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.384% African / African-American · 288/75,040 alleles

Filtering AF 0.347% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.333%

Overall 0.0219% 353/1,614,102 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.384%	261
Middle Eastern	0.066%	1,516
Remaining individualsnot grpmax-eligible	0.0592%	1,689
Admixed American	0.0183%	5,457
South Asian	0.00659%	15,177
European (non-Finnish)	0.000593%	168,567

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.Ala349=
Coding: c.1047A>T
MANE Select: NM_145054
dbSNP: rs113576151
Type: single nucleotide variant
Location: chr17:9628693 (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.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
CFAP52 p.Tyr41His 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-ala349 (accessed [today's date]).

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