Is CTLA4 p.Tyr139Ter (c.417C>G) pathogenic?

CTLA4 p.Tyr139Ter (c.417C>G) is classified Likely pathogenic in CTLA4 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-16). Absent from gnomAD v4.1; Associated with CTLA4-related disorder.

What condition is associated with CTLA4 p.Tyr139Ter (c.417C>G)?

CTLA4 p.Tyr139Ter (c.417C>G) is associated with CTLA4-related disorder (ClinVar).

How common is CTLA4 p.Tyr139Ter (c.417C>G) in the general population?

CTLA4 p.Tyr139Ter (c.417C>G) is absent from gnomAD v4.1 (gnomAD).

CTLA4 p.Tyr139Ter

c.417C>G · VCV4959470

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

CTLA4-related disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function in a LoF-intolerant gene
NMD	predicted	premature termination codon in exon 2 of 4
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.2	GERP 0.62, phastCons 1
Overall
CADD	35.0	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: CTLA4
Protein: p.Tyr139Ter
Coding: c.417C>G
MANE Select: NM_005214
Type: single nucleotide variant
Location: chr2:203870893 (GRCh38)
Gene constraint: LOEUF 0.211 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 79.67 · 22 PDB
Residue 139: the ig-like v-type domain; the 'important for interaction with cd80 and cd86' region

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

Disease context

CTLA4-related disorder

Similar variants

CTLA4 p.Tyr139Cys Likely pathogenic ★★★ same residue
CTLA4 p.Tyr139His Pathogenic ★ same residue
CTLA4 p.Tyr139Ser Likely pathogenic ★ same residue
CTLA4 p.Tyr139= Likely benign ★ same residue
CTLA4 c.110-2A>G Likely pathogenic ★ same condition
CTLA4 c.457+1G>A Likely pathogenic ★ same condition
CTLA4 p.Tyr127Cys Conflicting classifications of pathogenicity ★ ⚠ same condition
CTLA4 p.Gln12Ter 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/ctla4-p-tyr139ter (accessed [today's date]).

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