Is CFAP52 p.Ile79Phe (c.235A>T) pathogenic?

CFAP52 p.Ile79Phe (c.235A>T) is classified Uncertain significance in CFAP52 (ClinVar, Single submitter, 2 submitters; last evaluated 2023-05-09). AlphaMissense: ambiguous (0.371); Very rare (popmax 0.00834%, amr).

How common is CFAP52 p.Ile79Phe (c.235A>T) in the general population?

CFAP52 p.Ile79Phe (c.235A>T) is very rare (popmax 0.00834%, amr) (gnomAD).

What do computational predictors say about CFAP52 p.Ile79Phe (c.235A>T)?

AlphaMissense predicts ambiguous (score 0.371) — an in-silico prediction, not a clinical call.

CFAP52 p.Ile79Phe

c.235A>T · rs376170198 · VCV2662354

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

ambiguous

0.371 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00834%, amr)

Missense predictors

1/2 damaging

REVEL, SaProt · AlphaMissense no call

Computational evidence

Protein change
AlphaMissense	0.371	ambiguous
REVEL	0.209	benign-leaning
SaProt	LLR -12.30	damaging
⇒ SaProt calls this damaging; REVEL does not; AlphaMissense makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -0.5	GERP -3.8
Regional constraint	o/e 1.00	unconstrained · MANE · 66 kb · p 0.9 · regional, not allelic
Overall
CADD	12.78	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 0.00834% Admixed American · 5/59,962 alleles

Filtering AF 0.00323% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00207%

Overall 0.00211% 34/1,613,698 alleles · very rare

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	0.0608%	1,645
Remaining individualsnot grpmax-eligible	0.0112%	8,925
Admixed Americangrpmax	0.00834%	11,992
European (non-Finnish)	0.000339%	294,980

Ashkenazi Jewish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Ile79Phe
Coding: c.235A>T
MANE Select: NM_145054
dbSNP: rs376170198
Type: single nucleotide variant
Location: chr17:9585937 (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.Ile79= Likely benign ★★ same residue
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

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-ile79phe (accessed [today's date]).

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