Is CEBPB p.Pro15= (c.45G>A) pathogenic?

CEBPB p.Pro15= (c.45G>A) is classified Likely benign in CEBPB (ClinVar, Single submitter, 1 submitter; last evaluated 2018-06-12). Ultra-rare (popmax 0.0439%, afr).

How common is CEBPB p.Pro15= (c.45G>A) in the general population?

CEBPB p.Pro15= (c.45G>A) is ultra-rare (popmax 0.0439%, afr) (gnomAD).

CEBPB p.Pro15=

c.45G>A · rs541523592 · VCV744842

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0439%, afr)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 11	GERP 0.19, phastCons 1
Overall
CADD	12.95	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0439% African / African-American · 31/70,566 alleles

Filtering AF 0.0318% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0276%

Overall 0.00341% 53/1,553,898 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0439%	2,276
Remaining individualsnot grpmax-eligible	0.0334%	2,994
Admixed American	0.00365%	27,411

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: CEBPB
Protein: p.Pro15=
Coding: c.45G>A
MANE Select: NM_005194
dbSNP: rs541523592
Type: single nucleotide variant
Location: chr20:50191078 (GRCh38)
Gene constraint: LOEUF 1.677 · pLI 0.15 (gnomAD)
Structure: AlphaFold pLDDT 61.55 · 16 PDB
Residue 15: the 'required for lys-174 sumoylation' region

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

Similar variants

CEBPB p.Pro15Ser Uncertain significance ★ ⚠ same residue
CEBPB p.Ala103Thr Uncertain significance ★ ⚠ same type
CEBPB p.Ala103Val Uncertain significance ★ ⚠ same type
CEBPB p.Ala147Pro Uncertain significance ★ ⚠ same type
CEBPB p.Ala241Val Uncertain significance ★ ⚠ same type
CEBPB p.Ala247Val Uncertain significance ★ ⚠ same type
CEBPB p.Ala250Val Uncertain significance ★ ⚠ same type
CEBPB p.Ala253Thr 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/cebpb-p-pro15 (accessed [today's date]).

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