Is BTG2 p.Gln43Pro (c.128A>C) pathogenic?

BTG2 p.Gln43Pro (c.128A>C) is classified Likely benign in BTG2 (ClinVar, No assertion criteria, 1 submitter). AlphaMissense: likely pathogenic (0.8861); Absent from gnomAD v4.1; Associated with EBV-positive nodal T- and NK-cell lymphoma.

What condition is associated with BTG2 p.Gln43Pro (c.128A>C)?

BTG2 p.Gln43Pro (c.128A>C) is associated with EBV-positive nodal T- and NK-cell lymphoma (ClinVar).

How common is BTG2 p.Gln43Pro (c.128A>C) in the general population?

BTG2 p.Gln43Pro (c.128A>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about BTG2 p.Gln43Pro (c.128A>C)?

AlphaMissense predicts likely pathogenic (score 0.8861) — an in-silico prediction, not a clinical call.

BTG2 p.Gln43Pro

c.128A>C · rs1658242159 · VCV2681618

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8861 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

EBV-positive nodal T- and NK-cell lymphoma

Computational evidence

Protein change
AlphaMissense	0.8861	likely pathogenic
REVEL	0.277	benign-leaning
SaProt	LLR -14.99	damaging
⇒ AlphaMissense and SaProt call this damaging; REVEL does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 9.1	GERP 2.3, phastCons 1
Regional constraint	o/e 0.95	unconstrained · MANE · 1,828 bp · p 0.51 · regional, not allelic
Overall
CADD	29.3	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: BTG2
Protein: p.Gln43Pro
Coding: c.128A>C
MANE Select: NM_006763
dbSNP: rs1658242159
Type: single nucleotide variant
Location: chr1:203305734 (GRCh38)
Gene constraint: LOEUF 1.193 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.38 · 2 PDB
Residue 43: an α-helix

Full BTG2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

EBV-positive nodal T- and NK-cell lymphoma

Similar variants

BTG2 c.142+3G>A Likely benign same condition
BTG2 p.Glu44= Likely benign same condition
BTG2 p.Arg145Gly Uncertain significance ★ ⚠ same type
BTG2 p.Asp8Asn Uncertain significance ★ ⚠ same type
BTG2 p.Gln89Arg Uncertain significance ★ ⚠ same type
BTG2 p.Glu125Val Uncertain significance ★ ⚠ same type
BTG2 p.Glu32Gln Uncertain significance ★ ⚠ same type
BTG2 p.Gly4Arg 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/btg2-p-gln43pro (accessed [today's date]).

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