Is DLGAP1 p.Arg976fs (c.2925_2929del) pathogenic?

DLGAP1 p.Arg976fs (c.29252929del) is classified Uncertain significance in DLGAP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-06-12). No gnomAD frequency available for this variant; Associated with Inborn genetic diseases.

What condition is associated with DLGAP1 p.Arg976fs (c.2925_2929del)?

DLGAP1 p.Arg976fs (c.2925_2929del) is associated with Inborn genetic diseases (ClinVar).

How common is DLGAP1 p.Arg976fs (c.2925_2929del) in the general population?

DLGAP1 p.Arg976fs (c.2925_2929del) is no gnomAD frequency available for this variant (gnomAD).

DLGAP1 p.Arg976fs

c.2925_2929del · rs2049797649 · VCV985894

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a LoF-intolerant gene
NMD	escapes	premature termination codon in the last exon (13 of 13) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 9.1	GERP 2.5, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: DLGAP1
Protein: p.Arg976fs
Coding: c.2925_2929del
MANE Select: NM_004746
dbSNP: rs2049797649
Type: Deletion
Location: chr18:3499190 (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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

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-arg976fs (accessed [today's date]).

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