Is B3GNT8 p.Ser44Arg (c.132C>A) pathogenic?

B3GNT8 p.Ser44Arg (c.132C>A) is classified Uncertain significance in B3GNT8 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-06-24). AlphaMissense: likely benign (0.1211); Rare (popmax 0.141%, afr).

How common is B3GNT8 p.Ser44Arg (c.132C>A) in the general population?

B3GNT8 p.Ser44Arg (c.132C>A) is rare (popmax 0.141%, afr) (gnomAD).

What do computational predictors say about B3GNT8 p.Ser44Arg (c.132C>A)?

AlphaMissense predicts likely benign (score 0.1211) — an in-silico prediction, not a clinical call.

B3GNT8 p.Ser44Arg

c.132C>A · rs200740953 · VCV2227717

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1211 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.141%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1211	likely benign
REVEL	0.037	moderately benign-leaning
SaProt	LLR -6.99	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.1	GERP 1.4, phastCons 0.58
Overall
CADD	12.59	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.141% African / African-American · 106/75,036 alleles

Filtering AF 0.119% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.111%

Overall 0.00719% 116/1,613,558 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.141%	708
Admixed American	0.01%	9,999
Remaining individualsnot grpmax-eligible	0.0064%	15,615

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: B3GNT8
Protein: p.Ser44Arg
Coding: c.132C>A
MANE Select: NM_001009905 · reported on NM_001385648
dbSNP: rs200740953
Type: single nucleotide variant
Location: chr19:41426647 (GRCh38)
Structure: AlphaFold pLDDT 96.05

Full B3GNT8 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

B3GNTL1 p.Gln144Arg Uncertain significance ★★ ⚠ same type
B3GNT8 c.-32-113C>T Benign ★★ same type
B3GNT8 c.-32-43A>G Benign ★★ same type
B3GNT8 c.*7T>C Benign ★★ same type
B3GNT8 p.Ala200= Benign ★★ same type
B3GNT8 p.Glu24= Benign ★★ same type
B3GNT8 p.Leu131= Benign ★★ same type
B3GNT8 p.Ser137Gly Benign ★★ ⚠ 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/b3gnt8-p-ser44arg (accessed [today's date]).

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