Is DLG3 p.Arg507= (c.1521G>A) pathogenic?

DLG3 p.Arg507= (c.1521G>A) is classified Likely benign in DLG3 (ClinVar, Single submitter, 1 submitter; last evaluated 2026-02-16). Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with DLG3 p.Arg507= (c.1521G>A)?

DLG3 p.Arg507= (c.1521G>A) is associated with Inborn genetic diseases (ClinVar).

How common is DLG3 p.Arg507= (c.1521G>A) in the general population?

DLG3 p.Arg507= (c.1521G>A) is absent from gnomAD v4.1 (gnomAD).

DLG3 p.Arg507=

c.1521G>A · VCV4839883

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,176,942)

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 2.9	GERP -0.43, phastCons 1
Overall
CADD	13.08	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,176,942). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: DLG3
Protein: p.Arg507=
Coding: c.1521G>A
MANE Select: NM_021120
Type: single nucleotide variant
Location: chrX:70492107 (GRCh38)
Structure: AlphaFold pLDDT 74.35 · 3 PDB
Residue 507: the sh3 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-arg507 (accessed [today's date]).

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