Is B3GALNT2 p.Ser59= (c.177A>G) pathogenic?

B3GALNT2 p.Ser59= (c.177A>G) is classified Likely benign in B3GALNT2 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-07-14). Absent from gnomAD v4.1; Associated with muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 11.

How common is B3GALNT2 p.Ser59= (c.177A>G) in the general population?

B3GALNT2 p.Ser59= (c.177A>G) is absent from gnomAD v4.1 (gnomAD).

How is Walker-Warburg syndrome inherited?

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

B3GALNT2 p.Ser59=

Q: What condition is associated with B3GALNT2 p.Ser59= (c.177A>G)?

B3GALNT2 p.Ser59= (c.177A>G) is associated with muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 11 (ClinVar).

c.177A>G · rs2102863197 · VCV1109406

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 11

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 -1	GERP -0.62, phastCons 0.005
Overall
CADD	6.489	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: B3GALNT2
Protein: p.Ser59=
Coding: c.177A>G
MANE Select: NM_152490
dbSNP: rs2102863197
Type: single nucleotide variant
Location: chr1:235494764 (GRCh38)
Gene constraint: LOEUF 1.041 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 86.81

Full B3GALNT2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type a, 11 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Walker-Warburg syndrome (Orphanet):

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

Similar variants

B3GALNT2 c.113-1G>C Likely pathogenic ★★ same condition
B3GALNT2 c.1311+1G>A Likely pathogenic ★★ same condition
B3GALNT2 c.1311+1G>C Likely pathogenic ★★ same condition
B3GALNT2 c.1368+1G>C Pathogenic ★★ same condition
B3GALNT2 c.762+1G>A Likely pathogenic ★★ same condition
B3GALNT2 c.842-1G>A Likely pathogenic ★★ same condition
B3GALNT2 p.Arg143Ter Pathogenic/Likely pathogenic ★★ same condition
B3GALNT2 p.Arg150Ter Pathogenic ★★ 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/b3galnt2-p-ser59 (accessed [today's date]).

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