Is CTBP2 p.Ile406= (c.1218C>A) pathogenic?

CTBP2 p.Ile406= (c.1218C>A) is classified Likely benign in CTBP2 (ClinVar, Single submitter, 2 submitters; last evaluated 2023-08-01). Absent from gnomAD v4.1.

How common is CTBP2 p.Ile406= (c.1218C>A) in the general population?

CTBP2 p.Ile406= (c.1218C>A) is absent from gnomAD v4.1 (gnomAD).

CTBP2 p.Ile406=

c.1218C>A · rs796230948 · VCV1050373

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Absent

absent from gnomAD v4.1

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 4.4	GERP -0.7, phastCons 1
Overall
CADD	9.176	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.Ile406=
Coding: c.1218C>A
MANE Select: NM_001329
dbSNP: rs796230948
Type: single nucleotide variant
Location: chr10:124989638 (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

Similar variants

CTBP2 p.Ile406fs Uncertain significance same residue
CTBP2 c.58+11873C>T Benign ★★ same type
CTBP2 c.58+11963C>T Benign ★★ same type
CTBP2 c.58+12441C>T Benign ★★ same type
CTBP2 c.58+12475A>C Benign ★★ same type
CTBP2 p.Pro309= Benign ★★ same type
ZRANB1 p.Arg669Trp Uncertain significance ★ ⚠ same type
ZRANB1 p.Arg670Trp 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/ctbp2-p-ile406 (accessed [today's date]).

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