Is CPAP p.Glu1034fs (c.3100_3103del) pathogenic?

CPAP p.Glu1034fs (c.31003103del) is classified Pathogenic in CPAP (ClinVar, Single submitter, 1 submitter; last evaluated 2022-08-15). Very rare (popmax 0.0011%, nfe).

How common is CPAP p.Glu1034fs (c.3100_3103del) in the general population?

CPAP p.Glu1034fs (c.3100_3103del) is very rare (popmax 0.0011%, nfe) (gnomAD).

CPAP p.Glu1034fs

c.3100_3103del · rs767234515 · VCV1964703

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.0011%, 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 10 of 17
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.6	GERP 1.6, phastCons 1

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0011% European (non-Finnish) · 13/1,179,954 alleles

Filtering AF 0.000615% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000474%

Overall 0.00103% 15/1,461,834 alleles · very rare

Ancestry group	Frequency	1 in
Remaining individualsnot grpmax-eligible	0.0032%	31,254
European (non-Finnish)grpmax	0.0011%	90,766

Remaining individuals shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Glu1034fs
Coding: c.3100_3103del
MANE Select: NM_018451
dbSNP: rs767234515
Type: Microsatellite
Location: chr13:24892756 (GRCh38)
Structure: AlphaFold pLDDT 56.70 · 6 PDB
Residue 1034: the 'interaction with stil' region

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

Similar variants

CPAP p.Asp705_Ser706insTer Pathogenic ★★ same type
CPAP c.3704-14_3704-12del Benign ★★ same type
CPAP p.Arg723fs Likely pathogenic ★ same type
CPAP p.Cys735_Asp736delinsTer Likely pathogenic ★ same type
CPAP p.Gln89fs Likely pathogenic ★ same type
CPAP p.Lys44fs Pathogenic ★ same type
CPAP c.1078-6_1078-2del Uncertain significance ★ same type
CPAP p.568KE[1] 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-glu1034fs (accessed [today's date]).

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