Is CTCF p.Asn55= (c.165C>T) pathogenic?

CTCF p.Asn55= (c.165C>T) is classified Likely benign in CTCF (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-05-01). Ultra-rare (popmax 0.0462%, sas); Associated with Inborn genetic diseases.

What condition is associated with CTCF p.Asn55= (c.165C>T)?

CTCF p.Asn55= (c.165C>T) is associated with Inborn genetic diseases (ClinVar).

How common is CTCF p.Asn55= (c.165C>T) in the general population?

CTCF p.Asn55= (c.165C>T) is ultra-rare (popmax 0.0462%, sas) (gnomAD).

CTCF p.Asn55=

c.165C>T · rs149456343 · VCV1777445

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0462%, sas)

Conditions

Inborn genetic diseases

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 0.015	GERP -2.9, phastCons 0.9
Overall
CADD	6.983	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0462% South Asian · 42/90,974 alleles

Filtering AF 0.0351% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0312%

Overall 0.00485% 78/1,608,126 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0462%	2,166
Remaining individualsnot grpmax-eligible	0.00643%	15,545
European (non-Finnish)	0.00272%	36,718

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: CTCF
Protein: p.Asn55=
Coding: c.165C>T
MANE Select: NM_006565
dbSNP: rs149456343
Type: single nucleotide variant
Location: chr16:67610997 (GRCh38)
Gene constraint: LOEUF 0.205 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 59.45 · 21 PDB
Residue 55: 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

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CTCF p.Asn55Ser Uncertain significance ★ ⚠ same residue
CTCF c.782-1G>C Pathogenic/Likely pathogenic ★★ same condition
CTCF p.Arg368Cys Pathogenic ★★ same condition
CTCF p.Pro378Leu Pathogenic/Likely pathogenic ★★ same condition
CTCF p.Arg277Gln Uncertain significance ★★ ⚠ same condition
CTCF p.Cys299Arg Uncertain significance ★★ ⚠ same condition
CTCF p.Gly597Arg Uncertain significance ★★ ⚠ same condition
CTCF p.Gly657Arg Uncertain significance ★★ ⚠ 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-asn55 (accessed [today's date]).

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