Is DEK p.Asp39Glu (c.117C>G) pathogenic?

DEK p.Asp39Glu (c.117C>G) is classified Likely benign in DEK (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-06). AlphaMissense: likely benign (0.0653); Absent from gnomAD v4.1.

How common is DEK p.Asp39Glu (c.117C>G) in the general population?

DEK p.Asp39Glu (c.117C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DEK p.Asp39Glu (c.117C>G)?

AlphaMissense predicts likely benign (score 0.0653) — an in-silico prediction, not a clinical call.

DEK p.Asp39Glu

c.117C>G · VCV4010682

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0653 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0653	likely benign
REVEL	0.073	moderately benign-leaning
SaProt	LLR -4.29	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 -5.5	GERP -3.7
Regional constraint	o/e 0.97	unconstrained · MANE · 38 kb · p 0.48 · regional, not allelic
Overall
CADD	6.67	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: DEK
Protein: p.Asp39Glu
Coding: c.117C>G
MANE Select: NM_003472
Type: single nucleotide variant
Location: chr6:18263871 (GRCh38)
Gene constraint: LOEUF 0.768 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 66.18 · 6 PDB
Residue 39: the 'disordered' region

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

Similar variants

DEK p.Asp39Asn Uncertain significance ★ ⚠ same residue
DEK p.Ala18Gly Uncertain significance ★ ⚠ same type
DEK p.Ala214Val Uncertain significance ★ ⚠ same type
DEK p.Ala334Asp Uncertain significance ★ ⚠ same type
DEK p.Ala3Val Uncertain significance ★ ⚠ same type
DEK p.Ala7Thr Uncertain significance ★ ⚠ same type
DEK p.Ala81Glu Uncertain significance ★ ⚠ same type
DEK p.Arg208Gln Uncertain significance ★ ⚠ same type

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/dek-p-asp39glu (accessed [today's date]).

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