Is DLGAP1 p.Thr361= (c.1083G>C) pathogenic?

DLGAP1 p.Thr361= (c.1083G>C) is classified Benign in DLGAP1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-06-04). Common (popmax 25.4%, afr) — too common for a highly-penetrant pathogenic allele; Associated with DLGAP1-related disorder.

What condition is associated with DLGAP1 p.Thr361= (c.1083G>C)?

DLGAP1 p.Thr361= (c.1083G>C) is associated with DLGAP1-related disorder (ClinVar).

DLGAP1 p.Thr361=

Q: How common is DLGAP1 p.Thr361= (c.1083G>C) in the general population?

DLGAP1 p.Thr361= (c.1083G>C) is common (popmax 25.4%, afr) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.1083G>C · rs3786431 · VCV3060984

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Common

common (popmax 25.4%, afr) — too common for a highly-penetrant pathogenic allele

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 -1.6	GERP -8.4
Overall
CADD	2.988	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 25.4% African / African-American · 19,028/74,886 alleles

Filtering AF 25.1% ClinGen BA1/BS1 input FAF95, joint · FAF99 25%

Overall 4.99% 80,609/1,613,844 alleles · common

Ancestry group	Frequency	1 in
African / African-Americangrpmax	25.4%	4
South Asian	10.4%	10
Ashkenazi Jewishnot grpmax-eligible	8.02%	12
Admixed American	7.1%	14
East Asian	6.94%	14
Amishnot grpmax-eligible	6.69%	15
Remaining individualsnot grpmax-eligible	5.76%	17
Finnishnot grpmax-eligible	5.05%	20
Middle Eastern	3.66%	27
European (non-Finnish)	2.99%	33

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.Thr361=
Coding: c.1083G>C
MANE Select: NM_004746
dbSNP: rs3786431
Type: single nucleotide variant
Location: chr18:3814148 (GRCh38)
Gene constraint: LOEUF 0.224 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 50.85 · 3 PDB
Residue 361: the 'disordered' region

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-thr361 (accessed [today's date]).

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