Is CFAP52 p.Pro512Ala (c.1534C>G) pathogenic?

CFAP52 p.Pro512Ala (c.1534C>G) is classified Uncertain significance in CFAP52 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-03-07). AlphaMissense: likely benign (0.3358); Very rare (popmax 0.000124%).

How common is CFAP52 p.Pro512Ala (c.1534C>G) in the general population?

CFAP52 p.Pro512Ala (c.1534C>G) is very rare (popmax 0.000124%) (gnomAD).

What do computational predictors say about CFAP52 p.Pro512Ala (c.1534C>G)?

AlphaMissense predicts likely benign (score 0.3358) — an in-silico prediction, not a clinical call.

CFAP52 p.Pro512Ala

c.1534C>G · VCV3832349

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.3358 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000124%)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.3358	likely benign
REVEL	0.371	indeterminate
SaProt	LLR -12.38	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 5.8	GERP 1.7, phastCons 1
Regional constraint	o/e 1.00	unconstrained · MANE · 66 kb · p 0.9 · regional, not allelic
Overall
CADD	24.9	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 0.000124%

Overall 0.000124% 2/1,614,024 alleles · very rare

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.Pro512Ala
Coding: c.1534C>G
MANE Select: NM_145054
Type: single nucleotide variant
Location: chr17:9638670 (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

Similar variants

CFAP52 p.Ala147Thr Uncertain significance ★★ ⚠ same type
CFAP52 p.Ala161Asp Uncertain significance ★★ ⚠ same type
CFAP52 p.Arg106Gln Uncertain significance ★★ ⚠ same type
CFAP52 p.Arg170Gln Uncertain significance ★★ ⚠ same type
CFAP52 p.Arg594Cys Uncertain significance ★★ ⚠ same type
CFAP52 p.Gly343Ser Uncertain significance ★★ ⚠ same type
CFAP52 p.Gly534Ala Uncertain significance ★★ same type
CFAP52 p.Met551Thr Uncertain significance ★★ ⚠ same type

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-pro512ala (accessed [today's date]).

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