Is DTX2 p.Asp409Glu (c.1227T>G) pathogenic?

DTX2 p.Asp409Glu (c.1227T>G) is classified Uncertain significance in DTX2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-22). AlphaMissense: likely benign (0.0824); Ultra-rare (popmax 0.0545%, eas).

How common is DTX2 p.Asp409Glu (c.1227T>G) in the general population?

DTX2 p.Asp409Glu (c.1227T>G) is ultra-rare (popmax 0.0545%, eas) (gnomAD).

What do computational predictors say about DTX2 p.Asp409Glu (c.1227T>G)?

AlphaMissense predicts likely benign (score 0.0824) — an in-silico prediction, not a clinical call.

DTX2 p.Asp409Glu

c.1227T>G · VCV4838074

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0824 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0545%, eas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0824	likely benign
REVEL	0.048	moderately benign-leaning
SaProt	LLR -7.06	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 -0.24	GERP -2.1, phastCons 0.45
Regional constraint	o/e 0.06	constrained · MANE · 10 kb · p 1.4e-18 · regional, not allelic
Overall
CADD	11.82	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0545% East Asian · 19/34,880 alleles

Filtering AF 0.0357% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0296%

Overall 0.0226% 157/694,244 alleles · ultra-rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0545%	1,836
Ashkenazi Jewishnot grpmax-eligible	0.0528%	1,894
Remaining individualsnot grpmax-eligible	0.0425%	2,352
Finnishnot grpmax-eligible	0.0313%	3,200
European (non-Finnish)	0.0222%	4,503
African / African-American	0.00877%	11,408
Admixed American	0.00498%	20,066
South Asian	0.00336%	29,787

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: DTX2
Protein: p.Asp409Glu
Coding: c.1227T>G
MANE Select: NM_001102594
Type: single nucleotide variant
Location: chr7:76500517 (GRCh38)
Gene constraint: LOEUF 0.855 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 73.01 · 4 PDB
Residue 409: a β-strand

Full DTX2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

DTX2 p.Ala422= Likely benign ★★ same type
DTX2 p.Gly515= Likely benign ★★ same type
DTX2 p.Pro484= Benign ★★ same type
DTX2 p.Ala146Asp Uncertain significance ★ ⚠ same type
DTX2 p.Ala17Thr Uncertain significance ★ ⚠ same type
DTX2 p.Ala187Ser Uncertain significance ★ ⚠ same type
DTX2 p.Ala195Ser Uncertain significance ★ ⚠ same type
DTX2 p.Ala255Gly 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/dtx2-p-asp409glu (accessed [today's date]).

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