Is CFAP418 p.Pro30fs (c.89_99del) pathogenic?

CFAP418 p.Pro30fs (c.8999del) is classified Pathogenic in CFAP418 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-10-17). Absent from gnomAD.

How common is CFAP418 p.Pro30fs (c.89_99del) in the general population?

CFAP418 p.Pro30fs (c.89_99del) is absent from gnomAD (gnomAD).

CFAP418 p.Pro30fs

c.89_99del · rs2132171444 · VCV1681151

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 1 of 6
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.29	GERP -0.68

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

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CFAP418
Protein: p.Pro30fs
Coding: c.89_99del
MANE Select: NM_177965
dbSNP: rs2132171444
Type: Deletion
Location: chr8:95269091 (GRCh38)
Gene constraint: LOEUF 1.642 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 75.73
Residue 30: the 'required for interaction with fam161a' region; the 'disordered' region

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

Similar variants

CFAP418 p.Pro30Ala Uncertain significance ★ ⚠ same residue
CFAP418 p.Glu60fs Pathogenic/Likely pathogenic ★★ same type
CFAP418 c.375-10del Likely benign ★★ same type
CFAP418 p.Arg42fs Pathogenic ★ same type
CFAP418 p.Asn121fs Pathogenic ★ same type
CFAP418 p.Asp6fs Pathogenic ★ same type
CFAP418 p.Glu162fs Pathogenic ★ same type
CFAP418 p.Gly117fs Pathogenic ★ 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/cfap418-p-pro30fs (accessed [today's date]).

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