Is DLGAP2 p.Arg658= (c.1974C>T) pathogenic?

DLGAP2 p.Arg658= (c.1974C>T) is classified Benign in DLGAP2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-06-13). Low-frequency (popmax 1.13%, afr); Associated with DLGAP2-related disorder.

What condition is associated with DLGAP2 p.Arg658= (c.1974C>T)?

DLGAP2 p.Arg658= (c.1974C>T) is associated with DLGAP2-related disorder (ClinVar).

How common is DLGAP2 p.Arg658= (c.1974C>T) in the general population?

DLGAP2 p.Arg658= (c.1974C>T) is low-frequency (popmax 1.13%, afr) (gnomAD).

DLGAP2 p.Arg658=

c.1974C>T · rs199785303 · VCV3033446

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

low-frequency (popmax 1.13%, afr)

Conditions

DLGAP2-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.016	strongly benign-leaning
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -6.8	GERP -3.6
Overall
CADD	0.561	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.13% African / African-American · 840/74,380 alleles

Filtering AF 1.07% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.04%

Overall 0.0665% 1,059/1,593,500 alleles · low-frequency

Ancestry group	Frequency	1 in
African / African-Americangrpmax	1.13%	89
Middle Eastern	0.0992%	1,008
Remaining individualsnot grpmax-eligible	0.0939%	1,064
Admixed American	0.0684%	1,462
European (non-Finnish)	0.00939%	10,646
South Asian	0.0057%	17,529
Ashkenazi Jewishnot grpmax-eligible	0.00342%	29,202

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.Arg658=
Coding: c.1974C>T
MANE Select: NM_001346810
dbSNP: rs199785303
Type: single nucleotide variant
Location: chr8:1668492 (GRCh38)
Gene constraint: LOEUF 0.425 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 48.83
Residue 658: 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.Arg658Cys Uncertain significance ★ ⚠ same residue
DLGAP2 p.Arg658His Uncertain significance ★ ⚠ same residue
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

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-arg658 (accessed [today's date]).

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