Is DLGAP1 p.Pro971= (c.2913C>T) pathogenic?

DLGAP1 p.Pro971= (c.2913C>T) is classified Likely benign in DLGAP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-09-01). Very rare (popmax 8.52e-05%, nfe).

How common is DLGAP1 p.Pro971= (c.2913C>T) in the general population?

DLGAP1 p.Pro971= (c.2913C>T) is very rare (popmax 8.52e-05%, nfe) (gnomAD).

DLGAP1 p.Pro971=

c.2913C>T · rs2510074683 · VCV2648533

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 8.52e-05%, nfe)

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 0.086	GERP 0.71, phastCons 0.68
Overall
CADD	12.77	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.52e-05% European (non-Finnish) · 1/1,173,482 alleles

Overall 6.94e-05% 1/1,440,698 alleles · very rare

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.Pro971=
Coding: c.2913C>T
MANE Select: NM_004746
dbSNP: rs2510074683
Type: single nucleotide variant
Location: chr18:3499206 (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

Similar variants

DLGAP1 p.Ala659= Benign ★★ same type
DLGAP1 p.Pro824= Benign ★★ same type
DLGAP1 p.Ser296= Benign ★★ same type
DLGAP1 p.Thr284= Benign ★★ same type
DLGAP1 p.Thr624= Benign ★★ same type
DLGAP1 p.Ala173Val Uncertain significance ★ ⚠ same type
DLGAP1 p.Ala189Thr Uncertain significance ★ ⚠ same type
DLGAP1 p.Ala302Val Uncertain significance ★ ⚠ same type

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-pro971 (accessed [today's date]).

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