Is CFAP99 p.Gln436Arg (c.1307A>G) pathogenic?

CFAP99 p.Gln436Arg (c.1307A>G) is classified Uncertain significance in CFAP99 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-15). Absent from gnomAD v4.1.

How common is CFAP99 p.Gln436Arg (c.1307A>G) in the general population?

CFAP99 p.Gln436Arg (c.1307A>G) is absent from gnomAD v4.1 (gnomAD).

CFAP99 p.Gln436Arg

c.1307A>G · VCV3832466

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,514,358)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
REVEL	0.059	moderately benign-leaning
Splicing
SpliceAI	Δ0.85	acceptor loss · deltas
Pangolin	Δ0.34	loss · gain 0.27 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 7.6	GERP 1.8, phastCons 1
Regional constraint	o/e 1.08	unconstrained · MANE · 36 kb · p 0.016 · regional, not allelic
Overall
CADD	24.4	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,514,358). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CFAP99
Protein: p.Gln436Arg
Coding: c.1307A>G
MANE Select: NM_001193282
Type: single nucleotide variant
Location: chr4:2459110 (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-gln436arg (accessed [today's date]).

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