Is B3GLCT p.Phe60= (c.180C>T) pathogenic?

B3GLCT p.Phe60= (c.180C>T) is classified Likely benign in B3GLCT (ClinVar, Multiple submitters, 2 submitters; last evaluated 2019-12-31). Ultra-rare (popmax 0.0572%, sas); Associated with Peters plus syndrome.

What condition is associated with B3GLCT p.Phe60= (c.180C>T)?

B3GLCT p.Phe60= (c.180C>T) is associated with Peters plus syndrome (ClinVar).

How common is B3GLCT p.Phe60= (c.180C>T) in the general population?

B3GLCT p.Phe60= (c.180C>T) is ultra-rare (popmax 0.0572%, sas) (gnomAD).

B3GLCT p.Phe60=

c.180C>T · rs370978491 · VCV767428

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0572%, sas)

Conditions

Peters plus syndrome

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 2.7	GERP -1.9, phastCons 1
Overall
CADD	13.02	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0572% South Asian · 52/90,900 alleles

Filtering AF 0.0448% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0404%

Overall 0.0074% 119/1,607,206 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0572%	1,748
African / African-American	0.0107%	9,327
Remaining individualsnot grpmax-eligible	0.00642%	15,567
European (non-Finnish)	0.00451%	22,155
East Asian	0.00446%	22,420

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.Phe60=
Coding: c.180C>T
MANE Select: NM_194318
dbSNP: rs370978491
Type: single nucleotide variant
Location: chr13:31229204 (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 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
B3GLCT p.Asp469Tyr 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-phe60 (accessed [today's date]).

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