Is CPOX p.Pro51= (c.153T>G) pathogenic?

CPOX p.Pro51= (c.153T>G) is classified Likely benign in CPOX (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-05-02). Absent from gnomAD v4.1; Associated with CPOX-related disorder.

What condition is associated with CPOX p.Pro51= (c.153T>G)?

CPOX p.Pro51= (c.153T>G) is associated with CPOX-related disorder (ClinVar).

How common is CPOX p.Pro51= (c.153T>G) in the general population?

CPOX p.Pro51= (c.153T>G) is absent from gnomAD v4.1 (gnomAD).

CPOX p.Pro51=

c.153T>G · rs2472122665 · VCV3038176

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,341,524)

Conditions

CPOX-related disorder

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 -0.29	GERP -0.37, phastCons 0.004
Overall
CADD	7.804	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,341,524). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: CPOX
Protein: p.Pro51=
Coding: c.153T>G
MANE Select: NM_000097
dbSNP: rs2472122665
Type: single nucleotide variant
Location: chr3:98593352 (GRCh38)
Gene constraint: LOEUF 0.8 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 80.32 · 1 PDB
Residue 51: a UniProt-annotated variant site (in hcp); the 'disordered' region

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

Disease context

CPOX-related disorder

Similar variants

CPOX p.Pro51Ser Uncertain significance ★ ⚠ same residue
CPOX p.Cys239Ter Pathogenic ★★ same condition
CPOX p.Glu201Lys Pathogenic/Likely pathogenic ★★ same condition
CPOX p.Ala83Val Uncertain significance ★★ ⚠ same condition
CPOX p.Ala89Val Uncertain significance ★★ ⚠ same condition
CPOX p.Pro51fs Pathogenic ★ same residue
CPOX p.Ala81Gly Uncertain significance ★ ⚠ same condition
CPOX p.Arg332Gln Conflicting classifications of pathogenicity ★ ⚠ same condition

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/cpox-p-pro51 (accessed [today's date]).

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