Is CFAP418 p.Lys46= (c.138G>A) pathogenic?

CFAP418 p.Lys46= (c.138G>A) is classified Likely benign in CFAP418 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2022-01-04). Absent from gnomAD v4.1; Associated with CFAP418-related disorder.

What condition is associated with CFAP418 p.Lys46= (c.138G>A)?

CFAP418 p.Lys46= (c.138G>A) is associated with CFAP418-related disorder (ClinVar).

How common is CFAP418 p.Lys46= (c.138G>A) in the general population?

CFAP418 p.Lys46= (c.138G>A) is absent from gnomAD v4.1 (gnomAD).

CFAP418 p.Lys46=

c.138G>A · VCV3355126

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

CFAP418-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.12	GERP -3.2
Overall
CADD	5.097	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CFAP418
Protein: p.Lys46=
Coding: c.138G>A
MANE Select: NM_177965
Type: single nucleotide variant
Location: chr8:95269052 (GRCh38)
Gene constraint: LOEUF 1.642 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 75.73
Residue 46: the 'required for interaction with fam161a' region; the 'disordered' region

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-lys46 (accessed [today's date]).

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