Is CFAP418 p.Ser40= (c.120C>T) pathogenic?

CFAP418 p.Ser40= (c.120C>T) is classified Likely benign in CFAP418 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2022-04-12). Absent from gnomAD v4.1; Associated with CFAP418-related disorder.

What condition is associated with CFAP418 p.Ser40= (c.120C>T)?

CFAP418 p.Ser40= (c.120C>T) is associated with CFAP418-related disorder (ClinVar).

How common is CFAP418 p.Ser40= (c.120C>T) in the general population?

CFAP418 p.Ser40= (c.120C>T) is absent from gnomAD v4.1 (gnomAD).

CFAP418 p.Ser40=

c.120C>T · VCV3354263

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	<0.2	all four deltas below 0.2 · G>C here scores Δ0.27 · evaluated, not missing
Constraint at this position
Conservation	phyloP 2.2	GERP 0.53, phastCons 0.99
Overall
CADD	9.993	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.Ser40=
Coding: c.120C>T
MANE Select: NM_177965
Type: single nucleotide variant
Location: chr8:95269070 (GRCh38)
Gene constraint: LOEUF 1.642 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 75.73
Residue 40: 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.Ser40Arg Uncertain significance ★ ⚠ same residue
CFAP418 p.Ser40Gly Uncertain significance ★ ⚠ same residue
CFAP418 p.Ser40Thr Uncertain significance ★ ⚠ same residue
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

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-ser40 (accessed [today's date]).

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