Is B4GAT1 p.Pro51= (c.153G>A) pathogenic?

B4GAT1 p.Pro51= (c.153G>A) is classified Likely benign in B4GAT1 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-10-10). Very rare (popmax 8.57e-05%, nfe); Associated with muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13.

How common is B4GAT1 p.Pro51= (c.153G>A) in the general population?

B4GAT1 p.Pro51= (c.153G>A) is very rare (popmax 8.57e-05%, nfe) (gnomAD).

How is Walker-Warburg syndrome inherited?

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

B4GAT1 p.Pro51=

Q: What condition is associated with B4GAT1 p.Pro51= (c.153G>A)?

B4GAT1 p.Pro51= (c.153G>A) is associated with muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13 (ClinVar).

c.153G>A · rs2134975644 · VCV1078367

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 8.57e-05%, nfe)

Conditions

muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13

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 -2.1, phastCons 0.001
Overall
CADD	10.19	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.57e-05% European (non-Finnish) · 1/1,166,208 alleles

Overall 6.98e-05% 1/1,433,304 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: B4GAT1
Protein: p.Pro51=
Coding: c.153G>A
MANE Select: NM_006876
dbSNP: rs2134975644
Type: single nucleotide variant
Location: chr11:66347393 (GRCh38)
Gene constraint: LOEUF 0.898 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 88.46

Full B4GAT1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13 — 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

B4GAT1 p.Pro51Ser Uncertain significance ★ ⚠ same residue
B4GAT1 p.Pro51Leu Likely benign ★ same residue
B4GAT1 p.Ala126Val Uncertain significance ★★ ⚠ same condition
B4GAT1 p.Ala154Ser Uncertain significance ★★ ⚠ same condition
B4GAT1 p.Ala379Gly Uncertain significance ★★ ⚠ same condition
B4GAT1 p.Ala75Thr Uncertain significance ★★ ⚠ same condition
B4GAT1 p.Arg341His Uncertain significance ★★ ⚠ same condition
B4GAT1 p.Arg414Cys 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/b4gat1-p-pro51 (accessed [today's date]).

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