Is CFAP54 p.Phe1571fs (c.4713_4716del) pathogenic?

CFAP54 p.Phe1571fs (c.47134716del) is classified Likely pathogenic in CFAP54 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-03-01). Very rare (popmax 0.00448%, eas).

How common is CFAP54 p.Phe1571fs (c.4713_4716del) in the general population?

CFAP54 p.Phe1571fs (c.4713_4716del) is very rare (popmax 0.00448%, eas) (gnomAD).

CFAP54 p.Phe1571fs

c.4713_4716del · VCV3778415

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.00448%, eas)

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 35 of 68
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -1.8	GERP -4.1
Overall
CADD	26.6	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 0.00448% East Asian · 2/44,692 alleles

Filtering AF 0.000742% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000278%

Overall 0.000125% 2/1,595,718 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: CFAP54
Protein: p.Phe1571fs
Coding: c.4713_4716del
MANE Select: NM_001306084
Type: Deletion
Location: chr12:96649910 (GRCh38)
Gene constraint: LOEUF 0.928 · pLI <0.01 (gnomAD)

Full CFAP54 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CFAP54 p.Cys1993fs Pathogenic ★ same type
CFAP54 p.Phe1106fs 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/cfap54-p-phe1571fs (accessed [today's date]).

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