Is DLG3 p.Phe143= (c.429C>T) pathogenic?

DLG3 p.Phe143= (c.429C>T) is classified Conflicting classifications of pathogenicity in DLG3 (ClinVar, Conflicting submitters, 5 submitters; last evaluated 2024-11-20). Rare (popmax 0.39%, mid); Associated with Inborn genetic diseases.

What condition is associated with DLG3 p.Phe143= (c.429C>T)?

DLG3 p.Phe143= (c.429C>T) is associated with Inborn genetic diseases (ClinVar).

How common is DLG3 p.Phe143= (c.429C>T) in the general population?

DLG3 p.Phe143= (c.429C>T) is rare (popmax 0.39%, mid) (gnomAD).

DLG3 p.Phe143=

c.429C>T · rs144225009 · VCV210852

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 5 submitters

gnomAD v4.1

Rare

rare (popmax 0.39%, mid)

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 4.8	GERP 1.9, phastCons 1
Overall
CADD	13.46	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.39% Middle Eastern · 17/4,355 alleles

Filtering AF 0.249% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.205%

Overall 0.177% 2,139/1,209,847 alleles · rare

Ancestry group	Frequency	1 in
Middle Easterngrpmax	0.39%	256
European (non-Finnish)	0.216%	463
Finnishnot grpmax-eligible	0.18%	554
Remaining individualsnot grpmax-eligible	0.151%	661
Admixed American	0.0437%	2,289
African / African-American	0.0193%	5,191
South Asian	0.00352%	28,373

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.Phe143=
Coding: c.429C>T
MANE Select: NM_021120
dbSNP: rs144225009
Type: single nucleotide variant
Location: chrX:70449379 (GRCh38)
Structure: AlphaFold pLDDT 74.35 · 3 PDB
Residue 143: 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 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-phe143 (accessed [today's date]).

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