Is CPAP p.Ser936Gly (c.2806A>G) pathogenic?

CPAP p.Ser936Gly (c.2806A>G) is classified Benign/Likely benign in CPAP (ClinVar, Multiple submitters, 6 submitters; last evaluated 2025-09-11). AlphaMissense: likely benign (0.0742); Low-frequency (popmax 1.79%, eas); Associated with Seckel syndrome 4.

What condition is associated with CPAP p.Ser936Gly (c.2806A>G)?

CPAP p.Ser936Gly (c.2806A>G) is associated with Seckel syndrome 4, microcephaly 6, primary, autosomal recessive (ClinVar).

How common is CPAP p.Ser936Gly (c.2806A>G) in the general population?

CPAP p.Ser936Gly (c.2806A>G) is low-frequency (popmax 1.79%, eas) (gnomAD).

What do computational predictors say about CPAP p.Ser936Gly (c.2806A>G)?

AlphaMissense predicts likely benign (score 0.0742) — an in-silico prediction, not a clinical call.

CPAP p.Ser936Gly

c.2806A>G · rs75008861 · VCV158204

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 6 submitters

AlphaMissense

likely benign

0.0742 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 1.79%, eas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Seckel syndrome 4

Computational evidence

Protein change
AlphaMissense	0.0742	likely benign
REVEL	0.262	benign-leaning
SaProt	LLR -6.97	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 3.4	GERP 0.56, phastCons 1
Regional constraint	o/e 0.96	unconstrained · MANE · 30 kb · p 0.11 · regional, not allelic
Overall
CADD	19.19	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 1.79% East Asian · 801/44,868 alleles

Filtering AF 1.68% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.64%

Overall 0.0569% 919/1,614,176 alleles · low-frequency

Ancestry group	Frequency	1 in
East Asiangrpmax	1.79%	56
South Asian	0.078%	1,283
Remaining individualsnot grpmax-eligible	0.0704%	1,421
European (non-Finnish)	0.000254%	393,335

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.Ser936Gly
Coding: c.2806A>G
MANE Select: NM_018451
dbSNP: rs75008861
Type: single nucleotide variant
Location: chr13:24903945 (GRCh38)
Structure: AlphaFold pLDDT 56.70 · 6 PDB
Residue 936: the 'interaction with stil' 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

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CPAP p.Arg958Ter Pathogenic/Likely pathogenic ★★ same condition
CPAP p.Gln14Ter Pathogenic/Likely pathogenic ★★ same condition
CPAP p.Gln657Ter Pathogenic/Likely pathogenic ★★ same condition
CPAP p.Glu212Ter Pathogenic/Likely pathogenic ★★ same condition
CPAP p.Glu955Ter 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-ser936gly (accessed [today's date]).

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