Is DLGAP1 p.Cys464= (c.1392C>T) pathogenic?

DLGAP1 p.Cys464= (c.1392C>T) is classified Likely benign in DLGAP1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2023-02-02). Very rare (popmax 0.004%, afr); Associated with DLGAP1-related disorder.

What condition is associated with DLGAP1 p.Cys464= (c.1392C>T)?

DLGAP1 p.Cys464= (c.1392C>T) is associated with DLGAP1-related disorder (ClinVar).

How common is DLGAP1 p.Cys464= (c.1392C>T) in the general population?

DLGAP1 p.Cys464= (c.1392C>T) is very rare (popmax 0.004%, afr) (gnomAD).

DLGAP1 p.Cys464=

c.1392C>T · rs148434174 · VCV3054756

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.004%, afr)

Conditions

DLGAP1-related disorder

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 0.031	GERP -4.1, phastCons 0.44
Overall
CADD	10.31	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.004% African / African-American · 3/74,924 alleles

Filtering AF 0.00231% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00202%

Overall 0.00254% 41/1,613,804 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.004%	24,975
European (non-Finnish)	0.00314%	31,888
Admixed American	0.00167%	59,996

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: DLGAP1
Protein: p.Cys464=
Coding: c.1392C>T
MANE Select: NM_004746
dbSNP: rs148434174
Type: single nucleotide variant
Location: chr18:3729334 (GRCh38)
Gene constraint: LOEUF 0.224 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 50.85 · 3 PDB

Full DLGAP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

DLGAP1-related disorder

Similar variants

DLGAP1 p.Arg340Ter Uncertain significance ★ same condition
DLGAP1 p.Trp810Ter Uncertain significance ★ same condition
DLGAP1 p.Leu269Gln Uncertain significance ⚠ same condition
DLGAP1 p.Thr69Pro Uncertain significance ⚠ same condition
DLGAP1 c.1351-3C>T Likely benign same condition
DLGAP1 c.957+4405C>G Likely benign same condition
DLGAP1 c.957+4506C>T Likely benign same condition
DLGAP1 c.957+4508T>C Benign 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/dlgap1-p-cys464 (accessed [today's date]).

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