Is B3GLCT p.Ser368= (c.1104C>T) pathogenic?

B3GLCT p.Ser368= (c.1104C>T) is classified Conflicting classifications of pathogenicity in B3GLCT (ClinVar, Conflicting submitters, 4 submitters; last evaluated 2025-12-03). Ultra-rare (popmax 0.0495%, mid); Associated with Peters plus syndrome.

What condition is associated with B3GLCT p.Ser368= (c.1104C>T)?

B3GLCT p.Ser368= (c.1104C>T) is associated with Peters plus syndrome (ClinVar).

How common is B3GLCT p.Ser368= (c.1104C>T) in the general population?

B3GLCT p.Ser368= (c.1104C>T) is ultra-rare (popmax 0.0495%, mid) (gnomAD).

B3GLCT p.Ser368=

c.1104C>T · rs114425388 · VCV283910

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0495%, mid)

Conditions

Peters plus syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · C>A here scores Δ0.42 · evaluated, not missing
Constraint at this position
Conservation	phyloP -0.67	GERP -1.7
Overall
CADD	5.833	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0495% Middle Eastern · 3/6,062 alleles

Filtering AF 0.0134% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00976%

Overall 0.0177% 285/1,614,032 alleles · ultra-rare

Ancestry group	Frequency	1 in
Ashkenazi Jewishnot grpmax-eligible	0.54%	185
Middle Easterngrpmax	0.0495%	2,021
Remaining individualsnot grpmax-eligible	0.048%	2,083
South Asian	0.0187%	5,357
Admixed American	0.0133%	7,502
East Asian	0.00669%	14,951
European (non-Finnish)	0.00525%	19,032
African / African-American	0.00267%	37,518

Ashkenazi Jewish 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: B3GLCT
Protein: p.Ser368=
Coding: c.1104C>T
MANE Select: NM_194318
dbSNP: rs114425388
Type: single nucleotide variant
Location: chr13:31317605 (GRCh38)
Gene constraint: LOEUF 1.109 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.94 · 1 PDB

Full B3GLCT gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Peters plus syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

B3GLCT p.Ser368Ala Uncertain significance ★ ⚠ same residue
B3GLCT c.459+1G>A Pathogenic/Likely pathogenic ★★ same condition
B3GLCT c.660+1G>A Pathogenic ★★ same condition
B3GLCT p.Tyr380Ter Pathogenic/Likely pathogenic ★★ same condition
B3GLCT c.*1752C>T Uncertain significance ★★ same condition
B3GLCT p.Arg377His Uncertain significance ★★ ⚠ same condition
B3GLCT p.Asn243Ser Uncertain significance ★★ ⚠ same condition
B3GLCT p.Asp469Asn 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/b3glct-p-ser368 (accessed [today's date]).

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