Is CPAP p.Arg985Thr (c.2954G>C) pathogenic?

CPAP p.Arg985Thr (c.2954G>C) is classified Uncertain significance in CPAP (ClinVar, Single submitter, 1 submitter; last evaluated 2023-08-04). AlphaMissense: likely pathogenic (0.5763); Absent from gnomAD v4.1.

How common is CPAP p.Arg985Thr (c.2954G>C) in the general population?

CPAP p.Arg985Thr (c.2954G>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CPAP p.Arg985Thr (c.2954G>C)?

AlphaMissense predicts likely pathogenic (score 0.5763) — an in-silico prediction, not a clinical call.

CPAP p.Arg985Thr

c.2954G>C · rs2541660779 · VCV2104387

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.5763 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.5763	likely pathogenic
REVEL	0.46	indeterminate
SaProt	LLR -9.12	tolerated
⇒ AlphaMissense calls this damaging; SaProt does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 1.4, phastCons 1
Regional constraint	o/e 0.96	unconstrained · MANE · 30 kb · p 0.11 · regional, not allelic
Overall
CADD	24.2	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

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CPAP
Protein: p.Arg985Thr
Coding: c.2954G>C
MANE Select: NM_018451
dbSNP: rs2541660779
Type: single nucleotide variant
Location: chr13:24899456 (GRCh38)
Structure: AlphaFold pLDDT 56.70 · 6 PDB
Residue 985: the 'interaction with stil' region

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

Similar variants

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
CPAP p.Gln657Ter 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-arg985thr (accessed [today's date]).

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