Is B3GNT9 p.Pro284Ser (c.850C>T) pathogenic?

B3GNT9 p.Pro284Ser (c.850C>T) is classified Uncertain significance in B3GNT9 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-11-11). AlphaMissense: likely pathogenic (0.9352); Absent from gnomAD v4.1.

How common is B3GNT9 p.Pro284Ser (c.850C>T) in the general population?

B3GNT9 p.Pro284Ser (c.850C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about B3GNT9 p.Pro284Ser (c.850C>T)?

AlphaMissense predicts likely pathogenic (score 0.9352) — an in-silico prediction, not a clinical call.

B3GNT9 p.Pro284Ser

c.850C>T · VCV4644927

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9352 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,601,122)

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.9352	likely pathogenic
REVEL	0.702	pathogenic-leaning
SaProt	LLR -14.76	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 12	GERP 2, phastCons 1
Regional constraint	o/e 1.12	unconstrained · MANE · 1,205 bp · p 0.0043 · regional, not allelic
Overall
CADD	28.4	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — 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

No allele count reported in gnomAD v4.1 (AN 1,601,122). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: B3GNT9
Protein: p.Pro284Ser
Coding: c.850C>T
MANE Select: NM_033309
Type: single nucleotide variant
Location: chr16:67149636 (GRCh38)
Gene constraint: LOEUF 1.94 · pLI 0.02 (gnomAD)
Structure: AlphaFold pLDDT 83.11

Full B3GNT9 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

B3GNT9 p.Ala134Val Uncertain significance ★ ⚠ same type
B3GNT9 p.Ala180Val Uncertain significance ★ ⚠ same type
B3GNT9 p.Ala196Asp Uncertain significance ★ ⚠ same type
B3GNT9 p.Ala213Gly Uncertain significance ★ ⚠ same type
B3GNT9 p.Ala213Val Uncertain significance ★ ⚠ same type
B3GNT9 p.Ala217Pro Uncertain significance ★ ⚠ same type
B3GNT9 p.Ala287Gly Uncertain significance ★ ⚠ same type
B3GNT9 p.Ala305Gly 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/b3gnt9-p-pro284ser (accessed [today's date]).

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