Is DLG3 p.Arg211= (c.633A>G) pathogenic?

DLG3 p.Arg211= (c.633A>G) is classified Likely benign in DLG3 (ClinVar, Single submitter, 1 submitter; last evaluated 2020-04-10). Ultra-rare (popmax 0.02%, amr); Associated with Inborn genetic diseases.

What condition is associated with DLG3 p.Arg211= (c.633A>G)?

DLG3 p.Arg211= (c.633A>G) is associated with Inborn genetic diseases (ClinVar).

How common is DLG3 p.Arg211= (c.633A>G) in the general population?

DLG3 p.Arg211= (c.633A>G) is ultra-rare (popmax 0.02%, amr) (gnomAD).

DLG3 p.Arg211=

c.633A>G · rs750963382 · VCV1752935

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.02%, amr)

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 0.049	GERP -3.7, phastCons 0.001
Overall
CADD	8.205	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.02% Admixed American · 9/45,066 alleles

Filtering AF 0.0104% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00776%

Overall 0.000747% 9/1,204,913 alleles · ultra-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.Arg211=
Coding: c.633A>G
MANE Select: NM_021120
dbSNP: rs750963382
Type: single nucleotide variant
Location: chrX:70449789 (GRCh38)
Structure: AlphaFold pLDDT 74.35 · 3 PDB
Residue 211: the pdz 1 domain; a β-strand

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 residue
DLG3 p.Arg211Gln Uncertain significance ★ ⚠ same residue
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-arg211 (accessed [today's date]).

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