Is CTLA4 p.Phe162fs (c.485del) pathogenic?

CTLA4 p.Phe162fs (c.485del) is classified Pathogenic in CTLA4 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2026-02-25). Associated with CTLA4 Haploinsufficiency.

What condition is associated with CTLA4 p.Phe162fs (c.485del)?

CTLA4 p.Phe162fs (c.485del) is associated with CTLA4 Haploinsufficiency (ClinVar).

CTLA4 p.Phe162fs

c.485del · VCV4849498

Pathogenic No assertion criteria

Classification

Pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

CTLA4 Haploinsufficiency

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 LoF-intolerant gene
NMD	predicted	premature termination codon in exon 3 of 4
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -2	GERP -0.6

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

Variant & gene context

Gene: CTLA4
Protein: p.Phe162fs
Coding: c.485del
MANE Select: NM_005214
Type: Deletion
Location: chr2:203871404 (GRCh38)
Gene constraint: LOEUF 0.211 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 79.67 · 22 PDB

Full CTLA4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

CTLA4 Haploinsufficiency

Similar variants

CTLA4 p.Phe56fs Likely pathogenic ★ same condition
CTLA4 c.110-2A>G Likely pathogenic ★ same condition
CTLA4 c.457+1G>A Likely pathogenic ★ same condition
CTLA4 p.Tyr139Ter Likely pathogenic ★ same condition
CTLA4 p.Tyr127Cys Conflicting classifications of pathogenicity ★ ⚠ same condition
CTLA4 p.Gln12Ter Pathogenic same condition
CTLA4 p.Pro154= Likely benign same condition
CTLA4 p.Ala121fs 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/ctla4-p-phe162fs (accessed [today's date]).

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