Is CEBPZ p.Thr33Ser (c.97A>T) pathogenic?

CEBPZ p.Thr33Ser (c.97A>T) is classified Uncertain significance in CEBPZ (ClinVar, Single submitter, 1 submitter; last evaluated 2021-11-23). AlphaMissense: likely benign (0.0654); Ultra-rare (popmax 0.0223%, eas).

How common is CEBPZ p.Thr33Ser (c.97A>T) in the general population?

CEBPZ p.Thr33Ser (c.97A>T) is ultra-rare (popmax 0.0223%, eas) (gnomAD).

What do computational predictors say about CEBPZ p.Thr33Ser (c.97A>T)?

AlphaMissense predicts likely benign (score 0.0654) — an in-silico prediction, not a clinical call.

CEBPZ p.Thr33Ser

c.97A>T · rs778829475 · VCV2254498

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0654 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0223%, eas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0654	likely benign
REVEL	0.016	strongly benign-leaning
SaProt	LLR -5.20	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 -0.11	GERP -2.8
Regional constraint	o/e 1.17	unconstrained · MANE · 30 kb · p 4.9e-09 · regional, not allelic
Overall
CADD	0.044	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 0.0223% East Asian · 10/44,890 alleles

Filtering AF 0.012% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00916%

Overall 0.00062% 10/1,614,046 alleles · ultra-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: CEBPZ
Protein: p.Thr33Ser
Coding: c.97A>T
MANE Select: NM_005760
dbSNP: rs778829475
Type: single nucleotide variant
Location: chr2:37231471 (GRCh38)
Gene constraint: LOEUF 0.923 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 67.34
Residue 33: the 'disordered' region

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

Similar variants

CEBPZ p.Ala1008Thr Uncertain significance ★ ⚠ same type
CEBPZ p.Ala2Ser Uncertain significance ★ ⚠ same type
CEBPZ p.Ala2Val Uncertain significance ★ ⚠ same type
CEBPZ p.Ala365Val Uncertain significance ★ ⚠ same type
CEBPZ p.Ala369Ser Uncertain significance ★ ⚠ same type
CEBPZ p.Ala382Val Uncertain significance ★ ⚠ same type
CEBPZ p.Ala3Ser Uncertain significance ★ ⚠ same type
CEBPZ p.Ala3Val 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/cebpz-p-thr33ser (accessed [today's date]).

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