Is TRA2B p.Tyr151His (c.451T>C) pathogenic?

TRA2B p.Tyr151His (c.451T>C) is classified Uncertain significance in TRA2B (ClinVar, Single submitter, 1 submitter; last evaluated 2024-09-18). AlphaMissense: likely pathogenic (0.978); Absent from gnomAD v4.1.

How common is TRA2B p.Tyr151His (c.451T>C) in the general population?

TRA2B p.Tyr151His (c.451T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about TRA2B p.Tyr151His (c.451T>C)?

AlphaMissense predicts likely pathogenic (score 0.978) — an in-silico prediction, not a clinical call.

TRA2B p.Tyr151His

c.451T>C · VCV3774643

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.978 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Computational evidence

Protein change
AlphaMissense	0.978	likely pathogenic
REVEL	0.619	indeterminate
SaProt	LLR -13.98	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 2.4, phastCons 1
Regional constraint	o/e 0.13	constrained · MANE · 4,333 bp · p 2.2e-28 · regional, not allelic
Overall
CADD	29.5	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

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: TRA2B
Protein: p.Tyr151His
Coding: c.451T>C
MANE Select: NM_004593
Type: single nucleotide variant
Location: chr3:185923867 (GRCh38)
Gene constraint: LOEUF 0.528 · pLI 0.96 (gnomAD)
Structure: AlphaFold pLDDT 57.18 · 4 PDB
Residue 151: the rrm domain; a β-strand

Full TRA2B gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

TRA2B c.170+1G>A Pathogenic ★ same type
TRA2B p.Gln7Ter Pathogenic ★ same type
TRA2B p.Thr201Met Pathogenic ★ same type
TRA2B c.171-2A>G Uncertain significance ★ same type
TRA2B c.782+5G>A Uncertain significance ★ same type
TRA2B p.Ala17Pro Uncertain significance ★ ⚠ same type
TRA2B p.Arg74His Uncertain significance ★ ⚠ same type
TRA2B p.Arg82His 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/tra2b-p-tyr151his (accessed [today's date]).

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