Is B4GAT1 p.Ser52= (c.156C>T) pathogenic?

B4GAT1 p.Ser52= (c.156C>T) is classified Likely benign in B4GAT1 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-18). Very rare (popmax 0.00111%, nfe); Associated with muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13.

How common is B4GAT1 p.Ser52= (c.156C>T) in the general population?

B4GAT1 p.Ser52= (c.156C>T) is very rare (popmax 0.00111%, nfe) (gnomAD).

How is Walker-Warburg syndrome inherited?

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

B4GAT1 p.Ser52=

Q: What condition is associated with B4GAT1 p.Ser52= (c.156C>T)?

B4GAT1 p.Ser52= (c.156C>T) is associated with muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A13 (ClinVar).

c.156C>T · rs767852256 · VCV1118061

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00111%, 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 0.48	GERP -2.1, phastCons 0.99
Overall
CADD	10.28	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00111% European (non-Finnish) · 13/1,166,998 alleles

Filtering AF 0.000622% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000479%

Overall 0.00216% 31/1,434,850 alleles · very rare

Ancestry group	Frequency	1 in
Finnishnot grpmax-eligible	0.0292%	3,428
European (non-Finnish)grpmax	0.00111%	89,769

Finnish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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.Ser52=
Coding: c.156C>T
MANE Select: NM_006876
dbSNP: rs767852256
Type: single nucleotide variant
Location: chr11:66347390 (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.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
B4GAT1 p.Asp91Asn Uncertain significance ★★ ⚠ same condition
B4GAT1 p.Gln194His 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-ser52 (accessed [today's date]).

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