Is CTCF p.Thr204fs (c.610dup) pathogenic?

CTCF p.Thr204fs (c.610dup) is classified Pathogenic in CTCF (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-09-25). Ultra-rare (gnomAD MAF 6.72e-06); Associated with desmoplastic/nodular medulloblastoma.

What condition is associated with CTCF p.Thr204fs (c.610dup)?

CTCF p.Thr204fs (c.610dup) is associated with desmoplastic/nodular medulloblastoma (ClinVar).

How common is CTCF p.Thr204fs (c.610dup) in the general population?

CTCF p.Thr204fs (c.610dup) is ultra-rare (gnomAD MAF 6.72e-06) (gnomAD).

How is Medulloblastoma inherited?

Typically Not applicable (Orphanet). A genetic counselor can assess individual risk for a family.

CTCF p.Thr204fs

c.610dup · rs886041997 · VCV280869

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

ultra-rare (gnomAD MAF 6.72e-06)

Conditions

desmoplastic/nodular medulloblastoma

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 7.7	GERP 2.9, phastCons 1

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

Population frequency

dbSNP / gnomAD

Global frequency 0.000672% via dbSNP · ultra-rare

No ancestry breakdown or filtering allele frequency is available for this variant, so BA1/BS1 cannot be assessed from this figure alone.

Variant & gene context

Gene: CTCF
Protein: p.Thr204fs
Coding: c.610dup
MANE Select: NM_006565
dbSNP: rs886041997
Type: Duplication
Location: chr16:67611435 (GRCh38)
Gene constraint: LOEUF 0.205 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 59.45 · 21 PDB
Residue 204: the 'disordered' region; 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

desmoplastic/nodular medulloblastoma — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Medulloblastoma (Orphanet):

Inheritance: Not applicable
Onset: All ages
Prevalence: 1-9 / 1 000 000 (Europe)

Similar variants

CTCF p.Thr204Ser Uncertain significance ★ ⚠ same residue
CTCF p.Ala148fs Likely pathogenic ★ same type
CTCF p.Arg396fs Pathogenic ★ same type
CTCF p.Arg596fs Pathogenic ★ same type
CTCF p.Asp290fs Likely pathogenic ★ same type
CTCF p.Cys353fs Likely pathogenic ★ same type
CTCF p.Gln106fs Pathogenic ★ same type
CTCF p.Gly111fs Pathogenic ★ 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/ctcf-p-thr204fs (accessed [today's date]).

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