Is CPAP p.Arg723fs (c.2167_2168del) pathogenic?

CPAP p.Arg723fs (c.21672168del) is classified Likely pathogenic in CPAP (ClinVar, Single submitter, 1 submitter; last evaluated 2025-02-19). Very rare (popmax 0.000339%, nfe).

How common is CPAP p.Arg723fs (c.2167_2168del) in the general population?

CPAP p.Arg723fs (c.2167_2168del) is very rare (popmax 0.000339%, nfe) (gnomAD).

CPAP p.Arg723fs

c.2167_2168del · rs1064794036 · VCV419675

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 0.000339%, nfe)

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 7 of 17
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.38	GERP -0.97

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000339% European (non-Finnish) · 4/1,180,028 alleles

Filtering AF 7.9e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 5.4e-05%

Overall 0.000274% 4/1,461,880 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: CPAP
Protein: p.Arg723fs
Coding: c.2167_2168del
MANE Select: NM_018451
dbSNP: rs1064794036
Type: Microsatellite
Location: chr13:24905870 (GRCh38)
Structure: AlphaFold pLDDT 56.70 · 6 PDB
Residue 723: the 'disordered' region

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

Similar variants

CPAP p.Arg723Gly Uncertain significance ★★ ⚠ same residue
CPAP p.Asp705_Ser706insTer Pathogenic ★★ same type
CPAP c.3704-14_3704-12del Benign ★★ same type
CPAP p.Cys735_Asp736delinsTer Likely pathogenic ★ same type
CPAP p.Gln89fs Likely pathogenic ★ same type
CPAP p.Glu1034fs Pathogenic ★ same type
CPAP p.Lys44fs Pathogenic ★ same type
CPAP c.1078-6_1078-2del Uncertain significance ★ 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/cpap-p-arg723fs (accessed [today's date]).

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