Is DLG3 p.Ile692= (c.2076C>T) pathogenic?

DLG3 p.Ile692= (c.2076C>T) is classified Conflicting classifications of pathogenicity in DLG3 (ClinVar, Conflicting submitters, 3 submitters; last evaluated 2026-02-02). Low-frequency (popmax 1.23%, sas); Associated with Inborn genetic diseases.

What condition is associated with DLG3 p.Ile692= (c.2076C>T)?

DLG3 p.Ile692= (c.2076C>T) is associated with Inborn genetic diseases (ClinVar).

How common is DLG3 p.Ile692= (c.2076C>T) in the general population?

DLG3 p.Ile692= (c.2076C>T) is low-frequency (popmax 1.23%, sas) (gnomAD).

DLG3 p.Ile692=

c.2076C>T · rs535820581 · VCV210851

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 3 submitters

gnomAD v4.1

Rare

low-frequency (popmax 1.23%, sas)

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 -4.9	GERP -3.7
Overall
CADD	0.319	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.23% South Asian · 694/56,602 alleles

Filtering AF 1.15% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.12%

Overall 0.0614% 742/1,208,863 alleles · low-frequency

Ancestry group	Frequency	1 in
South Asiangrpmax	1.23%	82
Remaining individualsnot grpmax-eligible	0.0777%	1,286
Admixed American	0.00219%	45,685
European (non-Finnish)	0.00112%	89,459

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.Ile692=
Coding: c.2076C>T
MANE Select: NM_021120
dbSNP: rs535820581
Type: single nucleotide variant
Location: chrX:70499980 (GRCh38)
Structure: AlphaFold pLDDT 74.35 · 3 PDB
Residue 692: 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-ile692 (accessed [today's date]).

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