Is CTBP1 p.Phe42del (c.125_127del) pathogenic?

CTBP1 p.Phe42del (c.125127del) is classified Likely pathogenic in CTBP1 (ClinVar, Single submitter, 1 submitter; last evaluated 2020-10-16). Absent from gnomAD; Associated with intellectual disability.

What condition is associated with CTBP1 p.Phe42del (c.125_127del)?

CTBP1 p.Phe42del (c.125_127del) is associated with intellectual disability (ClinVar).

How common is CTBP1 p.Phe42del (c.125_127del) in the general population?

CTBP1 p.Phe42del (c.125_127del) is absent from gnomAD (gnomAD).

CTBP1 p.Phe42del

c.125_127del · rs1731781760 · VCV981895

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

intellectual disability

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.4	GERP 1.6, phastCons 1

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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: CTBP1
Protein: p.Phe42del
Coding: c.125_127del
MANE Select: NM_001012614
dbSNP: rs1731781760
Type: Deletion
Location: chr4:1238218 (GRCh38)
Gene constraint: LOEUF 0.533 · pLI 0.95 (gnomAD)
Structure: AlphaFold pLDDT 84.08 · 11 PDB
Residue 42: the 'interaction with glis2 1' region; an α-helix

Full CTBP1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

intellectual disability — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CTBP1 p.Phe42Ser Uncertain significance ★ ⚠ same residue
CTBP1 c.515-811_515-810del Uncertain significance ★ same type
CTBP1 c.989-6_989-4del Uncertain significance ★ same type
CTBP1 p.Ala45_Ser47del Uncertain significance ★ same type
CTBP1 c.162+296_162+330del Likely benign ★ same type
CTBP1 c.162+339_162+408del Likely benign ★ same type
CTBP1 c.162+892_162+961del Benign ★ same type
CTBP1 c.-189+14_-189+64del Likely benign ★ 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/ctbp1-p-phe42del (accessed [today's date]).

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