Is DLG3 p.Tyr760= (c.2280T>C) pathogenic?

DLG3 p.Tyr760= (c.2280T>C) is classified Likely benign in DLG3 (ClinVar, Single submitter, 1 submitter; last evaluated 2017-10-12). Very rare (popmax 0.000112%, nfe); Associated with Inborn genetic diseases.

What condition is associated with DLG3 p.Tyr760= (c.2280T>C)?

DLG3 p.Tyr760= (c.2280T>C) is associated with Inborn genetic diseases (ClinVar).

How common is DLG3 p.Tyr760= (c.2280T>C) in the general population?

DLG3 p.Tyr760= (c.2280T>C) is very rare (popmax 0.000112%, nfe) (gnomAD).

DLG3 p.Tyr760=

c.2280T>C · rs727503900 · VCV1788941

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.000112%, nfe)

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 -7.8	GERP -3.6
Overall
CADD	1.572	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000112% European (non-Finnish) · 1/891,064 alleles

Overall 9.17e-05% 1/1,090,052 alleles · very rare

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.Tyr760=
Coding: c.2280T>C
MANE Select: NM_021120
dbSNP: rs727503900
Type: single nucleotide variant
Location: chrX:70500922 (GRCh38)
Structure: AlphaFold pLDDT 74.35 · 3 PDB
Residue 760: 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.Tyr760Ter Pathogenic ★ same residue
DLG3 p.Tyr760His 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

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-tyr760 (accessed [today's date]).

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