Is CEBPD p.Arg169Gly (c.505A>G) pathogenic?

CEBPD p.Arg169Gly (c.505A>G) is classified Likely benign in CEBPD (ClinVar, Single submitter, 1 submitter; last evaluated 2021-08-12). AlphaMissense: likely benign (0.0453); Rare (popmax 0.318%, amr).

How common is CEBPD p.Arg169Gly (c.505A>G) in the general population?

CEBPD p.Arg169Gly (c.505A>G) is rare (popmax 0.318%, amr) (gnomAD).

What do computational predictors say about CEBPD p.Arg169Gly (c.505A>G)?

AlphaMissense predicts likely benign (score 0.0453) — an in-silico prediction, not a clinical call.

CEBPD p.Arg169Gly

c.505A>G · rs777407313 · VCV2367192

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0453 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.318%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0453	likely benign
REVEL	0.02	moderately benign-leaning
SaProt	LLR -5.28	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 0.59	GERP -3.6, phastCons 0.012
Regional constraint	o/e 1.00	unconstrained · MANE · 806 bp · p 0.97 · regional, not allelic
Overall
CADD	12.73	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.318% Admixed American · 76/23,916 alleles

Filtering AF 0.26% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.239%

Overall 0.0467% 612/1,311,028 alleles · rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.318%	315
Middle Eastern	0.0864%	1,158
European (non-Finnish)	0.0475%	2,105
Remaining individualsnot grpmax-eligible	0.0324%	3,084
South Asian	0.0249%	4,015
African / African-American	0.0201%	4,966
Ashkenazi Jewishnot grpmax-eligible	0.0106%	9,447

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: CEBPD
Protein: p.Arg169Gly
Coding: c.505A>G
MANE Select: NM_005195
dbSNP: rs777407313
Type: single nucleotide variant
Location: chr8:47737616 (GRCh38)
Gene constraint: LOEUF 0.99 · pLI 0.59 (gnomAD)
Structure: AlphaFold pLDDT 67.03
Residue 169: the 'disordered' region

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

Similar variants

CEBPD p.Ala12Gly Uncertain significance ★ ⚠ same type
CEBPD p.Ala12Thr Uncertain significance ★ ⚠ same type
CEBPD p.Ala130Val Uncertain significance ★ ⚠ same type
CEBPD p.Ala137Val Uncertain significance ★ ⚠ same type
CEBPD p.Ala173Val Uncertain significance ★ ⚠ same type
CEBPD p.Ala177Thr Uncertain significance ★ ⚠ same type
CEBPD p.Ala22Thr Uncertain significance ★ ⚠ same type
CEBPD p.Ala49Val 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/cebpd-p-arg169gly (accessed [today's date]).

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