Is CFAP52 p.Pro279Ser (c.835C>T) pathogenic?

CFAP52 p.Pro279Ser (c.835C>T) is classified Uncertain significance in CFAP52 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-04-20). AlphaMissense: likely benign (0.0875); Ultra-rare (popmax 0.0802%, afr).

How common is CFAP52 p.Pro279Ser (c.835C>T) in the general population?

CFAP52 p.Pro279Ser (c.835C>T) is ultra-rare (popmax 0.0802%, afr) (gnomAD).

What do computational predictors say about CFAP52 p.Pro279Ser (c.835C>T)?

AlphaMissense predicts likely benign (score 0.0875) — an in-silico prediction, not a clinical call.

CFAP52 p.Pro279Ser

c.835C>T · rs145130650 · VCV2347757

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0875 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0802%, afr)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0875	likely benign
REVEL	0.056	moderately benign-leaning
SaProt	LLR -10.37	damaging
⇒ SaProt calls this damaging; AlphaMissense and REVEL do not.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 4.8	GERP 1.7, phastCons 1
Regional constraint	o/e 1.00	unconstrained · MANE · 66 kb · p 0.9 · regional, not allelic
Overall
CADD	17.57	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 0.0802% African / African-American · 60/74,830 alleles

Filtering AF 0.0639% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.058%

Overall 0.00391% 63/1,610,020 alleles · ultra-rare exomes 32/1,457,988 · genomes 31/152,032 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0802%	1,247
Remaining individualsnot grpmax-eligible	0.00482%	20,734

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.Pro279Ser
Coding: c.835C>T
MANE Select: NM_145054
dbSNP: rs145130650
Type: single nucleotide variant
Location: chr17:9608200 (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-pro279ser (accessed [today's date]).

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