Is CFAP99 p.Arg304Gln (c.911G>A) pathogenic?

CFAP99 p.Arg304Gln (c.911G>A) is classified Uncertain significance in CFAP99 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-18). Very rare (popmax 0.00209%, nfe).

How common is CFAP99 p.Arg304Gln (c.911G>A) in the general population?

CFAP99 p.Arg304Gln (c.911G>A) is very rare (popmax 0.00209%, nfe) (gnomAD).

CFAP99 p.Arg304Gln

c.911G>A · VCV4001699

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00209%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.317	indeterminate
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>T here scores Δ0.20 · evaluated, not missing
Constraint at this position
Conservation	phyloP 11	GERP 0.93, phastCons 1
Regional constraint	o/e 1.08	unconstrained · MANE · 36 kb · p 0.016 · regional, not allelic
Overall
CADD	28.6	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00209% European (non-Finnish) · 24/1,146,866 alleles

Filtering AF 0.00142% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00119%

Overall 0.00573% 88/1,536,046 alleles · very rare

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	0.13%	768
Remaining individualsnot grpmax-eligible	0.005%	20,003
Ashkenazi Jewishnot grpmax-eligible	0.00349%	28,646
European (non-Finnish)grpmax	0.00209%	47,786
African / African-American	0.00137%	73,172
South Asian	0.00119%	84,040

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: CFAP99
Protein: p.Arg304Gln
Coding: c.911G>A
MANE Select: NM_001193282
Type: single nucleotide variant
Location: chr4:2451307 (GRCh38)
Gene constraint: LOEUF 1.203 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 77.28

Full CFAP99 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CFAP99 p.Ala255Thr Uncertain significance ★ same type
CFAP99 p.Ala307Thr Uncertain significance ★ same type
CFAP99 p.Ala366Thr Uncertain significance ★ same type
CFAP99 p.Ala369Gly Uncertain significance ★ same type
CFAP99 p.Ala396Val Uncertain significance ★ same type
CFAP99 p.Ala423Thr Uncertain significance ★ same type
CFAP99 p.Ala428Thr Uncertain significance ★ same type
CFAP99 p.Ala450Ser 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/cfap99-p-arg304gln (accessed [today's date]).

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