Is CPAP p.Arg1007Trp (c.3019C>T) pathogenic?

CPAP p.Arg1007Trp (c.3019C>T) is classified Uncertain significance in CPAP (ClinVar, Single submitter, 1 submitter; last evaluated 2015-08-12). AlphaMissense: likely benign (0.1736); Rare (popmax 0.101%, sas).

How common is CPAP p.Arg1007Trp (c.3019C>T) in the general population?

CPAP p.Arg1007Trp (c.3019C>T) is rare (popmax 0.101%, sas) (gnomAD).

What do computational predictors say about CPAP p.Arg1007Trp (c.3019C>T)?

AlphaMissense predicts likely benign (score 0.1736) — an in-silico prediction, not a clinical call.

CPAP p.Arg1007Trp

c.3019C>T · rs568294978 · VCV282558

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1736 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.101%, sas)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.1736	likely benign
REVEL	0.35	indeterminate
SaProt	LLR -11.79	damaging
⇒ SaProt calls this damaging; AlphaMissense does not; REVEL makes no call.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>C here scores Δ0.36 · evaluated, not missing
Constraint at this position
Conservation	phyloP 11	GERP 1.6, phastCons 1
Regional constraint	o/e 0.96	unconstrained · MANE · 30 kb · p 0.11 · regional, not allelic
Overall
CADD	29.0	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.101% South Asian · 92/90,898 alleles

Filtering AF 0.0844% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0783%

Overall 0.0111% 179/1,608,386 alleles · rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.101%	988
Remaining individualsnot grpmax-eligible	0.0321%	3,118
Middle Eastern	0.0165%	6,052
European (non-Finnish)	0.00561%	17,837

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.Arg1007Trp
Coding: c.3019C>T
MANE Select: NM_018451
dbSNP: rs568294978
Type: single nucleotide variant
Location: chr13:24892840 (GRCh38)
Structure: AlphaFold pLDDT 56.70 · 6 PDB
Residue 1007: the 'interaction with stil' region

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

Similar variants

CPAP p.Arg1007Gln Likely benign ★ same residue
CPAP c.2693-2A>G Likely pathogenic ★★ same type
CPAP p.Arg1298Gln Likely pathogenic ★★ same type
CPAP p.Arg378Ter Pathogenic ★★ same type
CPAP p.Arg566Ter Pathogenic/Likely pathogenic ★★ same type
CPAP p.Arg902Ter Pathogenic/Likely pathogenic ★★ same type
CPAP p.Arg958Ter Pathogenic/Likely pathogenic ★★ same type
CPAP p.Gln14Ter Pathogenic/Likely 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/cpap-p-arg1007trp (accessed [today's date]).

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