Is CPAP p.Pro411Ser (c.1231C>T) pathogenic?

CPAP p.Pro411Ser (c.1231C>T) is classified Uncertain significance in CPAP (ClinVar, Multiple submitters, 5 submitters; last evaluated 2025-11-17). AlphaMissense: likely benign (0.085); Ultra-rare (popmax 0.0262%, nfe); Associated with Seckel syndrome 4.

What condition is associated with CPAP p.Pro411Ser (c.1231C>T)?

CPAP p.Pro411Ser (c.1231C>T) is associated with Seckel syndrome 4, microcephaly 6, primary, autosomal recessive (ClinVar).

How common is CPAP p.Pro411Ser (c.1231C>T) in the general population?

CPAP p.Pro411Ser (c.1231C>T) is ultra-rare (popmax 0.0262%, nfe) (gnomAD).

What do computational predictors say about CPAP p.Pro411Ser (c.1231C>T)?

AlphaMissense predicts likely benign (score 0.085) — an in-silico prediction, not a clinical call.

CPAP p.Pro411Ser

c.1231C>T · rs145433187 · VCV434714

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 5 submitters

AlphaMissense

likely benign

0.085 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0262%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Seckel syndrome 4

Computational evidence

Protein change
AlphaMissense	0.085	likely benign
REVEL	0.09	moderately benign-leaning
SaProt	LLR -5.26	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.1	GERP -0.25, phastCons 0.43
Regional constraint	o/e 0.96	unconstrained · MANE · 30 kb · p 0.11 · regional, not allelic
Overall
CADD	0.201	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0262% European (non-Finnish) · 309/1,180,046 alleles

Filtering AF 0.0237% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0228%

Overall 0.0201% 325/1,614,052 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0262%	3,819
Remaining individualsnot grpmax-eligible	0.0096%	10,414
African / African-American	0.00801%	12,486
Admixed American	0.00333%	29,998
South Asian	0.0022%	45,544

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.Pro411Ser
Coding: c.1231C>T
MANE Select: NM_018451
dbSNP: rs145433187
Type: single nucleotide variant
Location: chr13:24906807 (GRCh38)
Structure: AlphaFold pLDDT 56.70 · 6 PDB
Residue 411: the 'disordered' region

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

Disease context

Seckel syndrome 4 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: microcephaly 6, primary, autosomal recessive

Similar variants

CPAP p.Pro411= Benign/Likely benign ★★ same residue
CPAP p.Pro411Leu Uncertain significance ★ ⚠ same residue
CPAP p.Arg1298Gln Likely pathogenic ★★ same condition
CPAP p.Arg378Ter Pathogenic ★★ same condition
CPAP p.Arg566Ter Pathogenic/Likely pathogenic ★★ same condition
CPAP p.Arg958Ter Pathogenic/Likely pathogenic ★★ same condition
CPAP p.Gln14Ter Pathogenic/Likely pathogenic ★★ same condition
CPAP p.Gln657Ter Pathogenic/Likely pathogenic ★★ same condition

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-pro411ser (accessed [today's date]).

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