Is BST2 p.Arg147Thr (c.440G>C) pathogenic?

BST2 p.Arg147Thr (c.440G>C) is classified Uncertain significance in BST2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-11-07). AlphaMissense: likely benign (0.1271); Very rare (popmax 0.00336%, amr).

How common is BST2 p.Arg147Thr (c.440G>C) in the general population?

BST2 p.Arg147Thr (c.440G>C) is very rare (popmax 0.00336%, amr) (gnomAD).

What do computational predictors say about BST2 p.Arg147Thr (c.440G>C)?

AlphaMissense predicts likely benign (score 0.1271) — an in-silico prediction, not a clinical call.

BST2 p.Arg147Thr

c.440G>C · VCV3482699

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1271 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00336%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1271	likely benign
REVEL	0.087	moderately benign-leaning
SaProt	LLR -5.92	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 -3.4	GERP -0.97
Regional constraint	o/e 0.80	unconstrained · MANE · 1,877 bp · p 0.0027 · regional, not allelic
Overall
CADD	5.908	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 0.00336% Admixed American · 2/59,606 alleles

Filtering AF 0.000557% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000208%

Overall 0.00041% 6/1,461,760 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00336%	29,803
Remaining individualsnot grpmax-eligible	0.0016%	62,458
European (non-Finnish)	0.000254%	393,227

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: BST2
Protein: p.Arg147Thr
Coding: c.440G>C
MANE Select: NM_004335
Type: single nucleotide variant
Location: chr19:17403798 (GRCh38)
Gene constraint: LOEUF 0.969 · pLI 0.01 (gnomAD)
Structure: AlphaFold pLDDT 85.63 · 15 PDB
Residue 147: an α-helix

Full BST2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BST2 p.Ala107Asp Uncertain significance ★ ⚠ same type
BST2 p.Ala163Thr Uncertain significance ★ ⚠ same type
BST2 p.Ala177Pro Uncertain significance ★ ⚠ same type
BST2 p.Arg10Ser Uncertain significance ★ ⚠ same type
BST2 p.Arg19Cys Uncertain significance ★ ⚠ same type
BST2 p.Arg19Gly Uncertain significance ★ ⚠ same type
BST2 p.Arg58Trp Uncertain significance ★ ⚠ same type
BST2 p.Asp159His 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/bst2-p-arg147thr (accessed [today's date]).

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