Is CTCF p.Val50fs (c.148dup) pathogenic?

CTCF p.Val50fs (c.148dup) is classified Pathogenic in CTCF (ClinVar, Single submitter, 1 submitter; last evaluated 2019-12-21). Absent from gnomAD; Associated with CTCF-related neurodevelopmental disorder.

What condition is associated with CTCF p.Val50fs (c.148dup)?

CTCF p.Val50fs (c.148dup) is associated with CTCF-related neurodevelopmental disorder (ClinVar).

How common is CTCF p.Val50fs (c.148dup) in the general population?

CTCF p.Val50fs (c.148dup) is absent from gnomAD (gnomAD).

How is CTCF-related neurodevelopmental disorder inherited?

Typically Autosomal dominant (Orphanet). A genetic counselor can assess individual risk for a family.

CTCF p.Val50fs

c.148dup · rs2142823841 · VCV1325769

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

CTCF-related neurodevelopmental disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 3 of 12
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 11	GERP 2.8, phastCons 1

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

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: CTCF
Protein: p.Val50fs
Coding: c.148dup
MANE Select: NM_006565
dbSNP: rs2142823841
Type: Duplication
Location: chr16:67610978 (GRCh38)
Gene constraint: LOEUF 0.205 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 59.45 · 21 PDB
Residue 50: a UniProt-annotated variant site (found in an endometrial carcinoma sample; uncertain significance)

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

Disease context

CTCF-related neurodevelopmental disorder — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For CTCF-related neurodevelopmental disorder (Orphanet):

Inheritance: Autosomal dominant
Onset: Antenatal, Childhood, Infancy, Neonatal

Similar variants

CTCF p.Ala148fs Likely pathogenic ★ same condition
CTCF p.Arg396fs Pathogenic ★ same condition
CTCF p.Asp290fs Likely pathogenic ★ same condition
CTCF p.Gly111fs Pathogenic ★ same condition
CTCF p.His541fs Pathogenic ★ same condition
CTCF p.Tyr25Ter Likely pathogenic ★ same condition
CTCF p.Val126fs Pathogenic ★ same condition
CTCF p.Val225fs Likely pathogenic ★ 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/ctcf-p-val50fs (accessed [today's date]).

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