Is DLGAP1 p.Ala783= (c.2349C>T) pathogenic?

DLGAP1 p.Ala783= (c.2349C>T) is classified Benign in DLGAP1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-02-20). Low-frequency (popmax 3.79%, afr); Associated with DLGAP1-related disorder.

What condition is associated with DLGAP1 p.Ala783= (c.2349C>T)?

DLGAP1 p.Ala783= (c.2349C>T) is associated with DLGAP1-related disorder (ClinVar).

How common is DLGAP1 p.Ala783= (c.2349C>T) in the general population?

DLGAP1 p.Ala783= (c.2349C>T) is low-frequency (popmax 3.79%, afr) (gnomAD).

DLGAP1 p.Ala783=

c.2349C>T · rs35715722 · VCV3056276

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

low-frequency (popmax 3.79%, 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 0.45	GERP -0.062, phastCons 0.99
Overall
CADD	10.31	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 3.79% African / African-American · 2,841/75,016 alleles

Filtering AF 3.67% ClinGen BA1/BS1 input FAF95, joint · FAF99 3.62%

Overall 1.83% 29,533/1,614,126 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	3.79%	26
South Asian	2.97%	34
Finnishnot grpmax-eligible	2.21%	45
Remaining individualsnot grpmax-eligible	1.91%	52
Middle Eastern	1.78%	56
European (non-Finnish)	1.72%	58
Ashkenazi Jewishnot grpmax-eligible	1.25%	80
Admixed American	1.07%	93
Amishnot grpmax-eligible	0.659%	152
East Asian	0.0267%	3,740

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.Ala783=
Coding: c.2349C>T
MANE Select: NM_004746
dbSNP: rs35715722
Type: single nucleotide variant
Location: chr18:3534324 (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-ala783 (accessed [today's date]).

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