Is DAG1 p.317TP[1] (c.954_959del) pathogenic?

DAG1 p.317TP[1] (c.954959del) is classified Uncertain significance in DAG1 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-07-12). Absent from gnomAD; Associated with muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A9.

How common is DAG1 p.317TP[1] (c.954_959del) in the general population?

DAG1 p.317TP[1] (c.954_959del) is absent from gnomAD (gnomAD).

How is Walker-Warburg syndrome inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

DAG1 p.317TP[1]

Q: What condition is associated with DAG1 p.317TP[1] (c.954_959del)?

DAG1 p.317TP[1] (c.954_959del) is associated with muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A9, autosomal recessive limb-girdle muscular dystrophy type 2P (ClinVar).

c.954_959del · rs2107931254 · VCV1366887

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A9

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.2	GERP -2.1, phastCons 0.14

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: DAG1
Protein: p.317TP[1]
Coding: c.954_959del
MANE Select: NM_004393
dbSNP: rs2107931254
Type: Deletion
Location: chr3:49531460 (GRCh38)
Gene constraint: LOEUF 0.298 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 68.44 · 8 PDB

Full DAG1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A9 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: autosomal recessive limb-girdle muscular dystrophy type 2P

For Walker-Warburg syndrome (Orphanet):

Inheritance: Autosomal recessive
Onset: Antenatal, Infancy, Neonatal
Prevalence: <1 / 1 000 000 (United Kingdom)

Similar variants

DAG1 c.286-10del Benign/Likely benign ★★ same condition
DAG1 p.Gln147fs Pathogenic ★ same condition
DAG1 p.Gln206fs Pathogenic ★ same condition
DAG1 p.Phe152fs Likely pathogenic ★ same condition
DAG1 p.Phe241fs Likely pathogenic ★ same condition
DAG1 c.286-1_287del Uncertain significance ★ same condition
DAG1 p.Arg454fs Uncertain significance ★ same condition
DAG1 p.Arg489fs Uncertain significance ★ 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/dag1-p-317tp-1 (accessed [today's date]).

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