Is CEBPG p.Ala37Ser (c.109G>T) pathogenic?

CEBPG p.Ala37Ser (c.109G>T) is classified Uncertain significance in CEBPG (ClinVar, Single submitter, 1 submitter; last evaluated 2025-08-05). AlphaMissense: likely benign (0.0834); Very rare (popmax 0.00667%, amr).

How common is CEBPG p.Ala37Ser (c.109G>T) in the general population?

CEBPG p.Ala37Ser (c.109G>T) is very rare (popmax 0.00667%, amr) (gnomAD).

What do computational predictors say about CEBPG p.Ala37Ser (c.109G>T)?

AlphaMissense predicts likely benign (score 0.0834) — an in-silico prediction, not a clinical call.

CEBPG p.Ala37Ser

c.109G>T · VCV4225091

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0834 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00667%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0834	likely benign
REVEL	0.167	moderately benign-leaning
SaProt	LLR -6.20	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 7.7	GERP 2.1, phastCons 1
Regional constraint	o/e 0.86	unconstrained · MANE · 449 bp · p 0.054 · regional, not allelic
Overall
CADD	21.5	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 0.00667% Admixed American · 4/60,008 alleles

Filtering AF 0.00226% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00135%

Overall 0.000248% 4/1,614,004 alleles · very rare exomes 4/1,461,758 · genomes 0/152,246 · joint denominator

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: CEBPG
Protein: p.Ala37Ser
Coding: c.109G>T
MANE Select: NM_001806
Type: single nucleotide variant
Location: chr19:33379348 (GRCh38)
Gene constraint: LOEUF 1.072 · pLI 0.04 (gnomAD)
Structure: AlphaFold pLDDT 76.64
Residue 37: the 'disordered' region

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

Similar variants

CEBPG p.Ala37Val Uncertain significance ★ ⚠ same residue
CEBPG p.Arg68Cys Uncertain significance ★ ⚠ same type
CEBPG p.Asp131Asn Uncertain significance ★ ⚠ same type
CEBPG p.Gln88Lys Uncertain significance ★ ⚠ same type
CEBPG p.Gly145Asp Uncertain significance ★ ⚠ same type
CEBPG p.Gly15Arg Uncertain significance ★ ⚠ same type
CEBPG p.Gly40Ala Uncertain significance ★ ⚠ same type
CEBPG p.Gly40Arg 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/cebpg-p-ala37ser (accessed [today's date]).

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