Is CFAP300 p.Phe67del (c.198_200del) pathogenic?

CFAP300 p.Phe67del (c.198200del) is classified Likely benign in CFAP300 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2024-09-17). Ultra-rare (popmax 0.0107%, nfe); Associated with CFAP300-related disorder.

What condition is associated with CFAP300 p.Phe67del (c.198_200del)?

CFAP300 p.Phe67del (c.198_200del) is associated with CFAP300-related disorder (ClinVar).

How common is CFAP300 p.Phe67del (c.198_200del) in the general population?

CFAP300 p.Phe67del (c.198_200del) is ultra-rare (popmax 0.0107%, nfe) (gnomAD).

CFAP300 p.Phe67del

c.198_200del · VCV3352549

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0107%, nfe)

Conditions

CFAP300-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.6	GERP 0.029, phastCons 1
Overall
CADD	16.9	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0107% European (non-Finnish) · 123/1,153,646 alleles

Filtering AF 0.00913% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00855%

Overall 0.0291% 455/1,562,404 alleles · ultra-rare

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	0.504%	198
Remaining individualsnot grpmax-eligible	0.0199%	5,024
European (non-Finnish)grpmax	0.0107%	9,379
Admixed American	0.00193%	51,936

Finnish 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: CFAP300
Protein: p.Phe67del
Coding: c.198_200del
MANE Select: NM_032930
Type: Deletion
Location: chr11:102058882 (GRCh38)
Gene constraint: LOEUF 1.386 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 94.21
Residue 67: a UniProt-annotated variant site (in cild38; loss of ciliary axoneme inner dynein arm and outer dynein arm structures in patient respiratory epithelial cells)

Full CFAP300 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

CFAP300-related disorder

Similar variants

CFAP300 p.Phe67fs Pathogenic ★★ same residue
CFAP300 p.His259Arg Pathogenic/Likely pathogenic ★★ same condition
CFAP300 p.Val263fs Likely pathogenic same condition
CFAP300 c.183_192+10del Pathogenic ★ 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/cfap300-p-phe67del (accessed [today's date]).

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