Is DLGAP2 p.Ala3Ser (c.7G>T) pathogenic?

DLGAP2 p.Ala3Ser (c.7G>T) is classified Benign in DLGAP2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-09-18). Low-frequency (popmax 3.14%, sas); Associated with DLGAP2-related disorder.

What condition is associated with DLGAP2 p.Ala3Ser (c.7G>T)?

DLGAP2 p.Ala3Ser (c.7G>T) is associated with DLGAP2-related disorder (ClinVar).

How common is DLGAP2 p.Ala3Ser (c.7G>T) in the general population?

DLGAP2 p.Ala3Ser (c.7G>T) is low-frequency (popmax 3.14%, sas) (gnomAD).

DLGAP2 p.Ala3Ser

c.7G>T · rs112628444 · VCV3039242

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

low-frequency (popmax 3.14%, sas)

Conditions

DLGAP2-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 3	GERP 0.42, phastCons 1
Overall
CADD	22.2	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 3.14% South Asian · 243/7,734 alleles

Filtering AF 2.82% ClinGen BA1/BS1 input FAF95, joint · FAF99 2.69%

Overall 0.993% 3,770/379,658 alleles · low-frequency

Ancestry group	Frequency	1 in
South Asiangrpmax	3.14%	32
Middle Eastern	1.77%	57
European (non-Finnish)	1.29%	78
Remaining individualsnot grpmax-eligible	1.04%	96
Admixed American	0.941%	106
Finnishnot grpmax-eligible	0.628%	159
Ashkenazi Jewishnot grpmax-eligible	0.567%	176
African / African-American	0.222%	451
East Asian	0.0225%	4,449

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: DLGAP2
Protein: p.Ala3Ser
Coding: c.7G>T
MANE Select: NM_001346810
dbSNP: rs112628444
Type: single nucleotide variant
Location: chr8:737814 (GRCh38)
Gene constraint: LOEUF 0.425 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 48.83

Full DLGAP2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

DLGAP2-related disorder

Similar variants

DLGAP2 p.Glu892Gln Uncertain significance ★ ⚠ same condition
DLGAP2 p.Asn662Thr Uncertain significance ⚠ same condition
DLGAP2 p.Leu192Val Uncertain significance ⚠ same condition
DLGAP2 p.Ser85Cys Uncertain significance ⚠ same condition
DLGAP2 c.107-10G>C Likely benign same condition
DLGAP2 c.1231-10C>G Likely benign same condition
DLGAP2 c.1810+10C>T Likely benign same condition
DLGAP2 c.2202+9C>T Likely 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/dlgap2-p-ala3ser (accessed [today's date]).

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