Is EP400 p.Val441= (c.1323T>C) pathogenic?

EP400 p.Val441= (c.1323T>C) is classified Likely benign in EP400 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2021-05-18). Absent from gnomAD v4.1; Associated with EP400-related disorder.

What condition is associated with EP400 p.Val441= (c.1323T>C)?

EP400 p.Val441= (c.1323T>C) is associated with EP400-related disorder (ClinVar).

How common is EP400 p.Val441= (c.1323T>C) in the general population?

EP400 p.Val441= (c.1323T>C) is absent from gnomAD v4.1 (gnomAD).

EP400 p.Val441=

c.1323T>C · rs1329649668 · VCV3054659

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,611,636)

Conditions

EP400-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · T>A here scores Δ0.57 · evaluated, not missing
Constraint at this position
Conservation	phyloP -0.62	phastCons 0.043
Overall
CADD	2.713	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,611,636). 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: EP400
Protein: p.Val441=
Coding: c.1323T>C
MANE Select: NM_015409
dbSNP: rs1329649668
Type: single nucleotide variant
Location: chr12:131961942 (GRCh38)
Gene constraint: LOEUF 0.365 · pLI 1.00 (gnomAD)

Full EP400 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

EP400-related disorder

Similar variants

EP400 p.Gly2702Glu Uncertain significance ★ same condition
EP400 p.Lys1297Arg Uncertain significance ★ same condition
EP400 p.Ser45Pro Uncertain significance ★ same condition
EP400 p.Ser573Phe Uncertain significance ★ same condition
EP400 c.2680-3C>A Uncertain significance same condition
EP400 c.4110+2T>A Uncertain significance same condition
EP400 c.5584+1G>A Uncertain significance same condition
EP400 p.Arg1295Ter Uncertain significance 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/ep400-p-val441 (accessed [today's date]).

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