B4GALT1 p.Ser64=
c.192G>A · rs763747159 · VCV741565
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00267%, afr)
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 -0.34 | GERP -1 |
| Overall | ||
| CADD | 11.02 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00267%
African / African-American · 2/74,848 alleles
Filtering AF
0.000443%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000166%
Overall
0.000349%
5/1,433,146 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00267% | 37,424 |
| European (non-Finnish) | 0.000256% | 390,892 |
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
- B4GALT1
- Protein
- p.Ser64=
- Coding
- c.192G>A
- MANE Select
- NM_001497
- dbSNP
- rs763747159
- Type
- single nucleotide variant
- Location
- chr9:33166978 (GRCh38)
- Gene constraint
- LOEUF 0.739 · pLI 0.02 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 85.23 · 19 PDB
- Residue 64
- the 'disordered' region
Similar variants
- B4GALT1 p.Ala17Val Uncertain significance ★★ ⚠ same type
- B4GALT1 p.Asp171Glu Uncertain significance ★★ ⚠ same type
- B4GALT1 p.Gly395Arg Uncertain significance ★★ ⚠ same type
- B4GALT1 p.His176Tyr Uncertain significance ★★ ⚠ same type
- B4GALT1 p.Ile180Val Uncertain significance ★★ ⚠ same type
- B4GALT1 p.Ile300Val Uncertain significance ★★ ⚠ same type
- B4GALT1 p.Met366Leu Uncertain significance ★★ ⚠ same type
- B4GALT1 p.Pro131Leu Uncertain significance ★★ ⚠ same type
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/b4galt1-p-ser64 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown