Is CFAP298 p.Thr66= (c.198C>T) pathogenic?

CFAP298 p.Thr66= (c.198C>T) is classified Benign/Likely benign in CFAP298 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-10-26). Very rare (popmax 0.00267%, afr).

How common is CFAP298 p.Thr66= (c.198C>T) in the general population?

CFAP298 p.Thr66= (c.198C>T) is very rare (popmax 0.00267%, afr) (gnomAD).

CFAP298 p.Thr66=

c.198C>T · rs139014235 · VCV2892362

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00267%, afr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.076	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -8.6	GERP -3
Overall
CADD	0.195	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00267% African / African-American · 2/74,950 alleles

Filtering AF 0.00172% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00149%

Overall 0.0189% 305/1,613,814 alleles · very rare

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	0.414%	241
Remaining individualsnot grpmax-eligible	0.0128%	7,811
African / African-Americangrpmax	0.00267%	37,475
European (non-Finnish)	0.00246%	40,684
South Asian	0.0011%	91,056

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: CFAP298
Protein: p.Thr66=
Coding: c.198C>T
MANE Select: NM_021254
dbSNP: rs139014235
Type: single nucleotide variant
Location: chr21:32609947 (GRCh38)
Gene constraint: LOEUF 1.267 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.54

Full CFAP298 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CFAP298 p.Arg98Ter Pathogenic/Likely pathogenic ★★ same type
CFAP298 p.Gln225Ter Pathogenic ★★ same type
CFAP298 p.Asp141Gly Uncertain significance ★★ ⚠ same type
CFAP298 p.Gln225Arg Uncertain significance ★★ ⚠ same type
CFAP298 p.Gly80Ser Uncertain significance ★★ ⚠ same type
CFAP298 c.308-16C>G Benign ★★ same type
CFAP298 c.375+15A>G Likely benign ★★ same type
CFAP298 c.376-20C>T Benign ★★ 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/cfap298-p-thr66 (accessed [today's date]).

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