Is DLG3 p.Ile613Val (c.1837A>G) pathogenic?

DLG3 p.Ile613Val (c.1837A>G) is classified Uncertain significance in DLG3 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-12). AlphaMissense: likely benign (0.0814); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with DLG3 p.Ile613Val (c.1837A>G)?

DLG3 p.Ile613Val (c.1837A>G) is associated with Inborn genetic diseases (ClinVar).

How common is DLG3 p.Ile613Val (c.1837A>G) in the general population?

DLG3 p.Ile613Val (c.1837A>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about DLG3 p.Ile613Val (c.1837A>G)?

AlphaMissense predicts likely benign (score 0.0814) — an in-silico prediction, not a clinical call.

DLG3 p.Ile613Val

c.1837A>G · VCV4241047

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0814 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0814	likely benign
REVEL	0.138	moderately benign-leaning
SaProt	LLR -5.82	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 9.4	GERP 0.78, phastCons 1
Regional constraint	o/e 0.71	unconstrained · MANE · 4,496 bp · p 0.022 · regional, not allelic
Overall
CADD	23.3	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: DLG3
Protein: p.Ile613Val
Coding: c.1837A>G
MANE Select: NM_021120
Type: single nucleotide variant
Location: chrX:70498537 (GRCh38)
Structure: AlphaFold pLDDT 74.35 · 3 PDB

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

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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-ile613val (accessed [today's date]).

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