Is CFAP418 p.Cys204= (c.612T>C) pathogenic?

CFAP418 p.Cys204= (c.612T>C) is classified Likely benign in CFAP418 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2024-07-12). Very rare (popmax 8.47e-05%, nfe); Associated with CFAP418-related disorder.

What condition is associated with CFAP418 p.Cys204= (c.612T>C)?

CFAP418 p.Cys204= (c.612T>C) is associated with CFAP418-related disorder (ClinVar).

How common is CFAP418 p.Cys204= (c.612T>C) in the general population?

CFAP418 p.Cys204= (c.612T>C) is very rare (popmax 8.47e-05%, nfe) (gnomAD).

CFAP418 p.Cys204=

c.612T>C · VCV3357513

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 8.47e-05%, nfe)

Conditions

CFAP418-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · A>T here scores Δ0.37 · evaluated, not missing
Pangolin	Δ0.21	gain · loss 0.00 · SpliceAI below 0.2 · independent
Constraint at this position
Conservation	phyloP -0.12	GERP -0.84, phastCons 0.003
Overall
CADD	4.806	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.47e-05% European (non-Finnish) · 1/1,180,036 alleles

Overall 6.84e-05% 1/1,461,850 alleles · very rare

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: CFAP418
Protein: p.Cys204=
Coding: c.612T>C
MANE Select: NM_177965
Type: single nucleotide variant
Location: chr8:95247629 (GRCh38)
Gene constraint: LOEUF 1.642 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 75.73

Full CFAP418 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

CFAP418-related disorder

Similar variants

CFAP418 p.Arg177Trp Pathogenic/Likely pathogenic ★★ same condition
CFAP418 p.Trp147Ter Pathogenic/Likely pathogenic ★★ same condition
CFAP418 p.Ala178Val Uncertain significance ★★ ⚠ same condition
CFAP418 p.Ala45Gly Uncertain significance ★★ ⚠ same condition
CFAP418 c.243+3A>C Likely pathogenic ★ same condition
CFAP418 c.375-1G>C Pathogenic ★ same condition
CFAP418 c.471-1G>T Likely pathogenic ★ same condition
CFAP418 c.374+1G>C Conflicting classifications of pathogenicity ★ 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/cfap418-p-cys204 (accessed [today's date]).

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