Is CFAP300 p.Val204Phe (c.610G>T) pathogenic?

CFAP300 p.Val204Phe (c.610G>T) is classified Uncertain significance in CFAP300 (ClinVar, Single submitter, 2 submitters; last evaluated 2021-08-05). AlphaMissense: likely pathogenic (0.8464); Very rare (popmax 0.00357%, nfe).

How common is CFAP300 p.Val204Phe (c.610G>T) in the general population?

CFAP300 p.Val204Phe (c.610G>T) is very rare (popmax 0.00357%, nfe) (gnomAD).

What do computational predictors say about CFAP300 p.Val204Phe (c.610G>T)?

AlphaMissense predicts likely pathogenic (score 0.8464) — an in-silico prediction, not a clinical call.

CFAP300 p.Val204Phe

c.610G>T · rs780254838 · VCV1681465

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely pathogenic

0.8464 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00357%, nfe)

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.8464	likely pathogenic
REVEL	0.645	pathogenic-leaning
SaProt	LLR -10.86	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 1.8, phastCons 1
Regional constraint	o/e 1.12	unconstrained · MANE · 36 kb · p 0.034 · regional, not allelic
Overall
CADD	29.5	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00357% European (non-Finnish) · 42/1,177,004 alleles

Filtering AF 0.00267% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00237%

Overall 0.00281% 45/1,603,652 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00357%	28,024
Remaining individualsnot grpmax-eligible	0.00322%	31,052
East Asian	0.00224%	44,696

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.Val204Phe
Coding: c.610G>T
MANE Select: NM_032930
dbSNP: rs780254838
Type: single nucleotide variant
Location: chr11:102081216 (GRCh38)
Gene constraint: LOEUF 1.386 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 94.21
Residue 204: 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

Similar variants

CFAP300 p.Arg121Ter Pathogenic ★★ same type
CFAP300 p.Arg144Ter Pathogenic/Likely pathogenic ★★ same type
CFAP300 p.Gln160Ter Pathogenic ★★ same type
CFAP300 p.Gln52Ter Pathogenic ★★ same type
CFAP300 p.His259Arg Pathogenic/Likely pathogenic ★★ same type
CFAP300 c.110+16A>G Benign ★★ same type
CFAP300 c.192+59A>C Benign ★★ same type
CFAP300 c.268+13T>C Benign/Likely 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/cfap300-p-val204phe (accessed [today's date]).

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