Is CFAP52 p.Ala71= (c.213C>T) pathogenic?

CFAP52 p.Ala71= (c.213C>T) is classified Benign/Likely benign in CFAP52 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2025-06-02). Rare (popmax 0.301%, nfe); Associated with situs inversus.

What condition is associated with CFAP52 p.Ala71= (c.213C>T)?

CFAP52 p.Ala71= (c.213C>T) is associated with situs inversus (ClinVar).

How common is CFAP52 p.Ala71= (c.213C>T) in the general population?

CFAP52 p.Ala71= (c.213C>T) is rare (popmax 0.301%, nfe) (gnomAD).

CFAP52 p.Ala71=

c.213C>T · rs143579503 · VCV772897

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

rare (popmax 0.301%, nfe)

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 0.25	GERP -0.055, phastCons 0.003
Overall
CADD	5.208	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.301% European (non-Finnish) · 3,552/1,179,866 alleles

Filtering AF 0.293% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.289%

Overall 0.242% 3,898/1,613,668 alleles · rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.301%	332
Remaining individualsnot grpmax-eligible	0.214%	466
Finnishnot grpmax-eligible	0.172%	581
Admixed American	0.0784%	1,276
Ashkenazi Jewishnot grpmax-eligible	0.0743%	1,345
African / African-American	0.04%	2,498
Middle Eastern	0.0165%	6,062
South Asian	0.0022%	45,530

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.Ala71=
Coding: c.213C>T
MANE Select: NM_145054
dbSNP: rs143579503
Type: single nucleotide variant
Location: chr17:9585915 (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-ala71 (accessed [today's date]).

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