Is CFAP300 p.Arg144Ter (c.430C>T) pathogenic?

CFAP300 p.Arg144Ter (c.430C>T) is classified Pathogenic/Likely pathogenic in CFAP300 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-05-22). Very rare (popmax 0.00331%, nfe); Associated with ciliary dyskinesia, primary, 38.

What condition is associated with CFAP300 p.Arg144Ter (c.430C>T)?

CFAP300 p.Arg144Ter (c.430C>T) is associated with ciliary dyskinesia, primary, 38 (ClinVar).

How common is CFAP300 p.Arg144Ter (c.430C>T) in the general population?

CFAP300 p.Arg144Ter (c.430C>T) is very rare (popmax 0.00331%, nfe) (gnomAD).

How is Primary ciliary dyskinesia inherited?

Typically Autosomal dominant, Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

CFAP300 p.Arg144Ter

c.430C>T · rs762224876 · VCV1676321

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.00331%, nfe)

Conditions

ciliary dyskinesia, primary, 38

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function
NMD	predicted	premature termination codon in exon 4 of 7
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>G here scores Δ0.20 · evaluated, not missing
Constraint at this position
Conservation	phyloP 1.6	GERP 0.71, phastCons 1
Overall
CADD	36.0	PHRED · no single calibrated threshold — expert panels disagree

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00331% European (non-Finnish) · 39/1,176,492 alleles

Filtering AF 0.00248% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00218%

Overall 0.00263% 42/1,599,148 alleles · very rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.00331%	30,166
Admixed American	0.00178%	56,148
Remaining individualsnot grpmax-eligible	0.00161%	62,046
South Asian	0.00116%	86,516

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.Arg144Ter
Coding: c.430C>T
MANE Select: NM_032930
dbSNP: rs762224876
Type: single nucleotide variant
Location: chr11:102066646 (GRCh38)
Gene constraint: LOEUF 1.386 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 94.21
Residue 144: 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

ciliary dyskinesia, primary, 38 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Primary ciliary dyskinesia (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive, X-linked recessive
Onset: Neonatal
Prevalence: 1-5 / 10 000 (Pakistan)

Similar variants

CFAP300 p.Arg121Ter Pathogenic ★★ same condition
CFAP300 p.Gln160Ter Pathogenic ★★ same condition
CFAP300 p.Gln52Ter Pathogenic ★★ same condition
CFAP300 p.His259Arg Pathogenic/Likely pathogenic ★★ same condition
CFAP300 c.110+16A>G Benign ★★ same condition
CFAP300 c.192+59A>C Benign ★★ same condition
CFAP300 p.Arg145Ter Pathogenic ★ same condition
CFAP300 p.Asp118Gly Likely pathogenic ★ ⚠ same condition

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-arg144ter (accessed [today's date]).

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