Is DLGAP2 p.Ile471= (c.1413C>T) pathogenic?

DLGAP2 p.Ile471= (c.1413C>T) is classified Likely benign in DLGAP2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-03-01). Rare (popmax 0.198%, nfe).

How common is DLGAP2 p.Ile471= (c.1413C>T) in the general population?

DLGAP2 p.Ile471= (c.1413C>T) is rare (popmax 0.198%, nfe) (gnomAD).

DLGAP2 p.Ile471=

c.1413C>T · rs201868215 · VCV2658292

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.198%, nfe)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
REVEL	0.017	moderately benign-leaning
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP -4.5	GERP -10
Overall
CADD	0.851	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.198% European (non-Finnish) · 2,334/1,178,508 alleles

Filtering AF 0.191% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.189%

Overall 0.161% 2,601/1,610,760 alleles · rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.198%	505
Finnishnot grpmax-eligible	0.132%	760
Remaining individualsnot grpmax-eligible	0.104%	960
South Asian	0.0797%	1,255
African / African-American	0.0387%	2,585
Middle Eastern	0.0335%	2,984
Admixed American	0.0168%	5,958
Ashkenazi Jewishnot grpmax-eligible	0.0135%	7,388
East Asian	0.00224%	44,694

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.Ile471=
Coding: c.1413C>T
dbSNP: rs201868215
Type: single nucleotide variant
Location: chr8:1565865 (GRCh38)

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

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-ile471 (accessed [today's date]).

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