Is EP300 p.Ser2366fs (c.7097del) pathogenic?

EP300 p.Ser2366fs (c.7097del) is classified Likely pathogenic in EP300 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-05-24). Absent from gnomAD; Associated with Inborn genetic diseases.

What condition is associated with EP300 p.Ser2366fs (c.7097del)?

EP300 p.Ser2366fs (c.7097del) is associated with Inborn genetic diseases (ClinVar).

How common is EP300 p.Ser2366fs (c.7097del) in the general population?

EP300 p.Ser2366fs (c.7097del) is absent from gnomAD (gnomAD).

EP300 p.Ser2366fs

c.7097del · rs2059220495 · VCV985034

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	escapes	premature termination codon in the last exon (31 of 31) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 6.2	GERP 2.5, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: EP300
Protein: p.Ser2366fs
Coding: c.7097del
MANE Select: NM_001429
dbSNP: rs2059220495
Type: Deletion
Location: chr22:41178808 (GRCh38)
Gene constraint: LOEUF 0.164 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 54.88 · 60 PDB
Residue 2366: the 'disordered' region

Full EP300 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

EP300 p.Ala1853_Pro1855del Uncertain significance ★★ same condition
EP300 c.3143-4del Benign/Likely benign ★★ same condition
EP300 p.Cys364fs Pathogenic ★ same condition
EP300 p.Glu1246fs Pathogenic ★ same condition
EP300 p.Gly194fs Pathogenic ★ same condition
EP300 p.Pro91fs Pathogenic ★ same condition
EP300 p.Thr1724fs Pathogenic ★ same condition
EP300 p.Thr1864fs 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/ep300-p-ser2366fs (accessed [today's date]).

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