Is CREBBP p.Cys1408Phe (c.4223G>T) pathogenic?

CREBBP p.Cys1408Phe (c.4223G>T) is classified Likely pathogenic in CREBBP (ClinVar, No assertion criteria, 1 submitter; last evaluated 2024-09-19). AlphaMissense: likely pathogenic (0.998); Absent from gnomAD v4.1; Associated with CREBBP-related disorder.

What condition is associated with CREBBP p.Cys1408Phe (c.4223G>T)?

CREBBP p.Cys1408Phe (c.4223G>T) is associated with CREBBP-related disorder (ClinVar).

How common is CREBBP p.Cys1408Phe (c.4223G>T) in the general population?

CREBBP p.Cys1408Phe (c.4223G>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CREBBP p.Cys1408Phe (c.4223G>T)?

AlphaMissense predicts likely pathogenic (score 0.998) — an in-silico prediction, not a clinical call.

CREBBP p.Cys1408Phe

c.4223G>T · VCV3346333

Likely pathogenic No assertion criteria

Classification

Likely pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.998 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

CREBBP-related disorder

Computational evidence

Protein change
AlphaMissense	0.998	likely pathogenic ✓ concordant with ClinVar · top 9% in CREBBP
REVEL	0.969	strongly pathogenic-leaning
SaProt	LLR -13.01	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 1.9, phastCons 1
Regional constraint	o/e 0.56	unconstrained · MANE · 22 kb · p 4.3e-21 · regional, not allelic
Overall
CADD	26.3	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: CREBBP
Protein: p.Cys1408Phe
Coding: c.4223G>T
MANE Select: NM_004380
Type: single nucleotide variant
Location: chr16:3739635 (GRCh38)
Gene constraint: LOEUF 0.101 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 54.31 · 144 PDB
Residue 1408: the cbp/p300-type hat domain

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

Disease context

CREBBP-related disorder

Similar variants

CREBBP c.1823+5G>A Pathogenic/Likely pathogenic ★★ same condition
CREBBP c.3779+1G>T Pathogenic ★★ same condition
CREBBP p.Arg1378Pro Pathogenic/Likely pathogenic ★★ same condition
CREBBP p.Arg1392Ter Pathogenic ★★ same condition
CREBBP p.Arg1867Trp Pathogenic/Likely pathogenic ★★ same condition
CREBBP p.Arg1868Gln Pathogenic/Likely pathogenic ★★ same condition
CREBBP p.Arg75Ter Pathogenic ★★ same condition
CREBBP p.Asp1480Gly 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/crebbp-p-cys1408phe (accessed [today's date]).

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