Is DLG3 p.Lys765= (c.2295G>A) pathogenic?

DLG3 p.Lys765= (c.2295G>A) is classified Benign/Likely benign in DLG3 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2017-11-21). Rare (popmax 0.307%, eas); Associated with Inborn genetic diseases.

What condition is associated with DLG3 p.Lys765= (c.2295G>A)?

DLG3 p.Lys765= (c.2295G>A) is associated with Inborn genetic diseases (ClinVar).

How common is DLG3 p.Lys765= (c.2295G>A) in the general population?

DLG3 p.Lys765= (c.2295G>A) is rare (popmax 0.307%, eas) (gnomAD).

DLG3 p.Lys765=

c.2295G>A · rs200152610 · VCV589107

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

rare (popmax 0.307%, 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
Constraint at this position
Conservation	phyloP 5.9	GERP -0.19, phastCons 1
Overall
CADD	9.301	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.307% East Asian · 102/33,231 alleles

Filtering AF 0.259% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.241%

Overall 0.00907% 109/1,202,155 alleles · rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.307%	326
Remaining individualsnot grpmax-eligible	0.0106%	9,457
South Asian	0.00181%	55,185
European (non-Finnish)	0.000112%	891,091

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.Lys765=
Coding: c.2295G>A
MANE Select: NM_021120
dbSNP: rs200152610
Type: single nucleotide variant
Location: chrX:70500937 (GRCh38)
Structure: AlphaFold pLDDT 74.35 · 3 PDB
Residue 765: the guanylate kinase-like domain

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.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
DLG3 p.His2Pro 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-lys765 (accessed [today's date]).

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