Is DLG3 p.Asp598= (c.1794C>T) pathogenic?

DLG3 p.Asp598= (c.1794C>T) is classified Likely benign in DLG3 (ClinVar, Single submitter, 1 submitter; last evaluated 2016-12-12). Very rare (popmax 0.00593%, eas); Associated with Inborn genetic diseases.

What condition is associated with DLG3 p.Asp598= (c.1794C>T)?

DLG3 p.Asp598= (c.1794C>T) is associated with Inborn genetic diseases (ClinVar).

How common is DLG3 p.Asp598= (c.1794C>T) in the general population?

DLG3 p.Asp598= (c.1794C>T) is very rare (popmax 0.00593%, eas) (gnomAD).

DLG3 p.Asp598=

c.1794C>T · rs1015617791 · VCV588548

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00593%, eas)

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Pangolin	Δ0.20	loss · gain 0.00 · not in the SpliceAI release · independent
Constraint at this position
Conservation	phyloP 7.5	GERP 1.6, phastCons 1
Overall
CADD	12.33	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00593% East Asian · 2/33,725 alleles

Filtering AF 0.000982% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000367%

Overall 0.000828% 10/1,208,198 alleles · very rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.00593%	16,862
African / African-American	0.00353%	28,368
Remaining individualsnot grpmax-eligible	0.0021%	47,576
European (non-Finnish)	0.000559%	178,906

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: DLG3
Protein: p.Asp598=
Coding: c.1794C>T
MANE Select: NM_021120
dbSNP: rs1015617791
Type: single nucleotide variant
Location: chrX:70495428 (GRCh38)
Structure: AlphaFold pLDDT 74.35 · 3 PDB

Full DLG3 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

DLG3 p.Asp598Asn Uncertain significance ★ ⚠ same residue
DLG3 p.Arg211Ter Pathogenic ★★ same condition
DLG3 p.Arg217Gln Uncertain significance ★★ ⚠ same condition
DLG3 p.Arg271Cys Uncertain significance ★★ ⚠ same condition
DLG3 p.Arg497Gln Uncertain significance ★★ ⚠ same condition
DLG3 p.Arg710Gln Uncertain significance ★★ ⚠ same condition
DLG3 p.Asp599Asn Uncertain significance ★★ ⚠ same condition
DLG3 p.Glu222Lys 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/dlg3-p-asp598 (accessed [today's date]).

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