B3GNT3 p.Pro44=
c.132C>T · rs79614823 · VCV769962
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.06%, 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 -4.3 | GERP -2.6 |
| Overall | ||
| CADD | 3.156 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.06%
African / African-American · 1,542/74,994 alleles
Filtering AF
1.97%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.94%
Overall
0.111%
1,793/1,613,396 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.06% | 49 |
| Middle Eastern | 0.693% | 144 |
| Ashkenazi Jewishnot grpmax-eligible | 0.21% | 477 |
| Remaining individualsnot grpmax-eligible | 0.117% | 856 |
| Admixed American | 0.1% | 1,000 |
| South Asian | 0.00329% | 30,356 |
| European (non-Finnish) | 0.000932% | 107,265 |
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
- B3GNT3
- Protein
- p.Pro44=
- Coding
- c.132C>T
- MANE Select
- NM_014256
- dbSNP
- rs79614823
- Type
- single nucleotide variant
- Location
- chr19:17807939 (GRCh38)
- Gene constraint
- LOEUF 1.03 · pLI 0.05 (gnomAD)
- Structure
- AlphaFold pLDDT 88.47
Similar variants
- B3GNT3 p.Thr319Met Benign ★★ ⚠ same type
- B3GNT3 p.Ala104Thr Uncertain significance ★ ⚠ same type
- B3GNT3 p.Ala16Val Uncertain significance ★ ⚠ same type
- B3GNT3 p.Ala281Thr Uncertain significance ★ ⚠ same type
- B3GNT3 p.Ala59Asp Uncertain significance ★ ⚠ same type
- B3GNT3 p.Ala63Thr Uncertain significance ★ ⚠ same type
- B3GNT3 p.Arg122Cys Uncertain significance ★ same type
- B3GNT3 p.Arg122Pro 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/b3gnt3-p-pro44 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown