Is CBFA2T3 p.Pro52Ser (c.154C>T) pathogenic?

CBFA2T3 p.Pro52Ser (c.154C>T) is classified Uncertain significance in CBFA2T3 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-05-13). AlphaMissense: likely benign (0.0724); Very rare (popmax 7.27e-05%).

How common is CBFA2T3 p.Pro52Ser (c.154C>T) in the general population?

CBFA2T3 p.Pro52Ser (c.154C>T) is very rare (popmax 7.27e-05%) (gnomAD).

What do computational predictors say about CBFA2T3 p.Pro52Ser (c.154C>T)?

AlphaMissense predicts likely benign (score 0.0724) — an in-silico prediction, not a clinical call.

CBFA2T3 p.Pro52Ser

c.154C>T · VCV3263615

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0724 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 7.27e-05%)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0724	likely benign
REVEL	0.1	moderately benign-leaning
SaProt	LLR -6.16	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>T here scores Δ0.26 · evaluated, not missing
Constraint at this position
Conservation	phyloP -0.57	GERP -2.3, phastCons 0.03
Regional constraint	o/e 1.12	unconstrained · MANE · 100 kb · p 0.00027 · regional, not allelic
Overall
CADD	6.647	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 7.27e-05%

Overall 7.27e-05% 1/1,374,952 alleles · very rare

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: CBFA2T3
Protein: p.Pro52Ser
Coding: c.154C>T
MANE Select: NM_005187
Type: single nucleotide variant
Location: chr16:88901654 (GRCh38)
Gene constraint: LOEUF 0.957 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 62.26 · 1 PDB
Residue 52: the 'mediates localization to the nucleus' region; a functional site (breakpoint for translocation to form type-1 runx1-cbfa2t3 fusion protein); the 'mediates interaction with pde7a (in isoform 2)' region; the 'required for nucleolar targeting (in isoform 1)' region; the 'disordered' region

Full CBFA2T3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

CBFA2T3 p.Ala441Thr Likely benign ★★ same type
CBFA2T3 p.Ala534= Benign ★★ same type
CBFA2T3 p.Ala141Val Uncertain significance ★ ⚠ same type
CBFA2T3 p.Ala272Thr Uncertain significance ★ ⚠ same type
CBFA2T3 p.Ala350Thr Uncertain significance ★ ⚠ same type
CBFA2T3 p.Ala449Thr Uncertain significance ★ ⚠ same type
CBFA2T3 p.Ala451Thr Uncertain significance ★ ⚠ same type
CBFA2T3 p.Ala460Pro 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/cbfa2t3-p-pro52ser (accessed [today's date]).

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