Is BTG2 p.Val141Met (c.421G>A) pathogenic?

BTG2 p.Val141Met (c.421G>A) is classified Uncertain significance in BTG2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2020-09-16). AlphaMissense: likely benign (0.0637); Absent from gnomAD v4.1.

How common is BTG2 p.Val141Met (c.421G>A) in the general population?

BTG2 p.Val141Met (c.421G>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about BTG2 p.Val141Met (c.421G>A)?

AlphaMissense predicts likely benign (score 0.0637) — an in-silico prediction, not a clinical call.

BTG2 p.Val141Met

c.421G>A · rs869320634 · VCV225129

Uncertain significance No assertion criteria

Classification

Uncertain significance

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0637 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0637	likely benign
REVEL	0.018	moderately benign-leaning
SaProt	LLR -7.40	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 3.5	GERP -1, phastCons 1
Regional constraint	o/e 0.95	unconstrained · MANE · 1,828 bp · p 0.51 · regional, not allelic
Overall
CADD	15.46	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

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.Val141Met
Coding: c.421G>A
MANE Select: NM_006763
dbSNP: rs869320634
Type: single nucleotide variant
Location: chr1:203307382 (GRCh38)
Gene constraint: LOEUF 1.193 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.38 · 2 PDB

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

Similar variants

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
BTG2 p.His3Asp Uncertain significance ★ ⚠ same type
BTG2 p.His53Asp 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-val141met (accessed [today's date]).

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