Is CTBP2 p.Pro314= (c.942G>C) pathogenic?

CTBP2 p.Pro314= (c.942G>C) is classified Likely benign in CTBP2 (ClinVar, No assertion criteria, 1 submitter). Absent from gnomAD v4.1; Associated with EBV-positive nodal T- and NK-cell lymphoma.

What condition is associated with CTBP2 p.Pro314= (c.942G>C)?

CTBP2 p.Pro314= (c.942G>C) is associated with EBV-positive nodal T- and NK-cell lymphoma (ClinVar).

How common is CTBP2 p.Pro314= (c.942G>C) in the general population?

CTBP2 p.Pro314= (c.942G>C) is absent from gnomAD v4.1 (gnomAD).

CTBP2 p.Pro314=

c.942G>C · rs74769610 · VCV2681218

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

EBV-positive nodal T- and NK-cell lymphoma

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 -2.9	GERP -4.8
Overall
CADD	3.804	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CTBP2
Protein: p.Pro314=
Coding: c.942G>C
MANE Select: NM_001329
dbSNP: rs74769610
Type: single nucleotide variant
Location: chr10:124993299 (GRCh38)
Gene constraint: LOEUF 0.522 · pLI 0.82 (gnomAD)
Structure: AlphaFold pLDDT 83.67 · 5 PDB
Residue 314: a β-strand

Full CTBP2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

EBV-positive nodal T- and NK-cell lymphoma

Similar variants

CTBP2 c.58+11243A>G Likely benign same condition
CTBP2 c.58+11362C>T Likely benign same condition
CTBP2 c.58+11426C>T Benign same condition
CTBP2 c.58+11458C>G Likely benign same condition
CTBP2 c.58+11546C>T Likely benign same condition
CTBP2 c.58+11702A>C Likely benign same condition
CTBP2 c.58+11874G>A Benign same condition
CTBP2 c.58+11883G>A Benign 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/ctbp2-p-pro314 (accessed [today's date]).

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