Is CTBP2 p.Arg13Ter (c.37C>T) pathogenic?

CTBP2 p.Arg13Ter (c.37C>T) is classified Likely benign in CTBP2 (ClinVar, No assertion criteria, 2 submitters). Absent from gnomAD v4.1; Associated with EBV-positive nodal T- and NK-cell lymphoma.

What condition is associated with CTBP2 p.Arg13Ter (c.37C>T)?

CTBP2 p.Arg13Ter (c.37C>T) is associated with EBV-positive nodal T- and NK-cell lymphoma (ClinVar).

How common is CTBP2 p.Arg13Ter (c.37C>T) in the general population?

CTBP2 p.Arg13Ter (c.37C>T) is absent from gnomAD v4.1 (gnomAD).

CTBP2 p.Arg13Ter

c.37C>T · rs1554881282 · VCV2681219

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 2 submitters

Consequence

nonsense (stop-gain)

predicted LoF

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.
Consequence	nonsense (stop-gain)	predicted loss-of-function
NMD	predicted	premature termination codon in exon 3 of 11
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · G>C here scores Δ0.23 · evaluated, not missing
Constraint at this position
Conservation	phyloP 9.6	GERP 2.2, phastCons 1
Overall
CADD	49.0	PHRED · no single calibrated threshold — expert panels disagree

Predicted loss-of-function is descriptive, not an applied PVS1 code.

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.Arg13Ter
Coding: c.37C>T
MANE Select: NM_001329
dbSNP: rs1554881282
Type: single nucleotide variant
Location: chr10:125039018 (GRCh38)
Gene constraint: LOEUF 0.522 · pLI 0.82 (gnomAD)
Structure: AlphaFold pLDDT 83.67 · 5 PDB

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-arg13ter (accessed [today's date]).

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