Is DLG4 p.Phe649fs (c.1947del) pathogenic?

DLG4 p.Phe649fs (c.1947del) is classified Likely pathogenic in DLG4 (ClinVar, Single submitter, 2 submitters; last evaluated 2024-04-04). Absent from gnomAD; Associated with intellectual developmental disorder 62.

What condition is associated with DLG4 p.Phe649fs (c.1947del)?

DLG4 p.Phe649fs (c.1947del) is associated with intellectual developmental disorder 62 (ClinVar).

How common is DLG4 p.Phe649fs (c.1947del) in the general population?

DLG4 p.Phe649fs (c.1947del) is absent from gnomAD (gnomAD).

DLG4 p.Phe649fs

c.1947del · rs2507910150 · VCV3236563

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

intellectual developmental disorder 62

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 18 of 20
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.8	GERP 2.4, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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: DLG4
Protein: p.Phe649fs
Coding: c.1947del
MANE Select: NM_001321075
dbSNP: rs2507910150
Type: Deletion
Location: chr17:7191922 (GRCh38)
Gene constraint: LOEUF 0.151 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 78.00 · 24 PDB
Residue 649: a UniProt-annotated variant site (in mrd62); the guanylate kinase-like domain

Full DLG4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

intellectual developmental disorder 62 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

DLG4 p.Asn114fs Pathogenic ★★ same condition
DLG4 p.Glu572fs Pathogenic/Likely pathogenic ★★ same condition
DLG4 p.Gly109fs Pathogenic ★★ same condition
DLG4 p.Lys202fs Pathogenic ★★ same condition
DLG4 p.Phe340fs Pathogenic/Likely pathogenic ★★ same condition
DLG4 p.Phe487fs Pathogenic ★★ same condition
DLG4 p.Thr566fs Pathogenic ★★ same condition
DLG4 p.Val619fs Pathogenic ★★ 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/dlg4-p-phe649fs (accessed [today's date]).

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