Is DTX2 p.Asn460Asp (c.1378A>G) pathogenic?

DTX2 p.Asn460Asp (c.1378A>G) is classified Uncertain significance in DTX2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-07-09). AlphaMissense: ambiguous (0.5387); Ultra-rare (popmax 0.0322%, nfe).

How common is DTX2 p.Asn460Asp (c.1378A>G) in the general population?

DTX2 p.Asn460Asp (c.1378A>G) is ultra-rare (popmax 0.0322%, nfe) (gnomAD).

What do computational predictors say about DTX2 p.Asn460Asp (c.1378A>G)?

AlphaMissense predicts ambiguous (score 0.5387) — an in-silico prediction, not a clinical call.

DTX2 p.Asn460Asp

c.1378A>G · rs150141824 · VCV2371246

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

ambiguous

0.5387 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0322%, nfe)

Missense predictors

1/2 damaging

REVEL, SaProt · AlphaMissense no call

Computational evidence

Protein change
AlphaMissense	0.5387	ambiguous
REVEL	0.231	benign-leaning
SaProt	LLR -11.81	damaging
⇒ SaProt calls this damaging; REVEL does not; AlphaMissense makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 1.8, phastCons 1
Regional constraint	o/e 0.88	unconstrained · MANE · 1,279 bp · p 0.18 · regional, not allelic
Overall
CADD	25.4	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

Grpmax group 0.0322% European (non-Finnish) · 380/1,179,852 alleles

Filtering AF 0.0295% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0284%

Overall 0.0252% 407/1,611,904 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0322%	3,105
Admixed American	0.015%	6,664
Remaining individualsnot grpmax-eligible	0.0144%	6,932
African / African-American	0.012%	8,337

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.Asn460Asp
Coding: c.1378A>G
MANE Select: NM_001102594
dbSNP: rs150141824
Type: single nucleotide variant
Location: chr7:76502445 (GRCh38)
Gene constraint: LOEUF 0.855 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 73.01 · 4 PDB
Residue 460: a turn

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-asn460asp (accessed [today's date]).

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