Is DLGAP2 p.Lys273= (c.819G>A) pathogenic?

DLGAP2 p.Lys273= (c.819G>A) is classified Likely benign in DLGAP2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-08-05). Very rare (popmax 0.00133%, afr); Associated with DLGAP2-related disorder.

What condition is associated with DLGAP2 p.Lys273= (c.819G>A)?

DLGAP2 p.Lys273= (c.819G>A) is associated with DLGAP2-related disorder (ClinVar).

How common is DLGAP2 p.Lys273= (c.819G>A) in the general population?

DLGAP2 p.Lys273= (c.819G>A) is very rare (popmax 0.00133%, afr) (gnomAD).

DLGAP2 p.Lys273=

c.819G>A · rs2485852737 · VCV3034880

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00133%, afr)

Conditions

DLGAP2-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.084	moderately benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.64	GERP 2.7, phastCons 0.92
Overall
CADD	4.473	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00133% African / African-American · 1/75,052 alleles

Filtering AF 6.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.9e-05%

Overall 0.000274% 4/1,459,020 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00133%	75,052
European (non-Finnish)	0.000254%	393,108

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.Lys273=
Coding: c.819G>A
MANE Select: NM_001346810
dbSNP: rs2485852737
Type: single nucleotide variant
Location: chr8:1549272 (GRCh38)
Gene constraint: LOEUF 0.425 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 48.83
Residue 273: the 'disordered' region

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-lys273 (accessed [today's date]).

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