Is CTLA4 p.Pro137Gln (c.410C>A) pathogenic?

CTLA4 p.Pro137Gln (c.410C>A) is classified Conflicting classifications of pathogenicity in CTLA4 (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2025-12-03). AlphaMissense: likely pathogenic (0.8883); Absent from gnomAD v4.1; Associated with autoimmune lymphoproliferative syndrome due to CTLA4 haploinsufficiency.

How common is CTLA4 p.Pro137Gln (c.410C>A) in the general population?

CTLA4 p.Pro137Gln (c.410C>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about CTLA4 p.Pro137Gln (c.410C>A)?

AlphaMissense predicts likely pathogenic (score 0.8883) — an in-silico prediction, not a clinical call.

CTLA4 p.Pro137Gln

Q: What condition is associated with CTLA4 p.Pro137Gln (c.410C>A)?

CTLA4 p.Pro137Gln (c.410C>A) is associated with autoimmune lymphoproliferative syndrome due to CTLA4 haploinsufficiency, Hashimoto thyroiditis, systemic lupus erythematosus (ClinVar).

Q: How is Autoimmune lymphoproliferative syndrome due to CTLA4 haploinsuffiency inherited?

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

c.410C>A · rs1553657429 · VCV574111

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely pathogenic

0.8883 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

autoimmune lymphoproliferative syndrome due to CTLA4 haploinsufficiency

Computational evidence

Protein change
AlphaMissense	0.8883	likely pathogenic · top 10% in CTLA4
REVEL	0.377	indeterminate
SaProt	LLR -10.82	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 1.5, phastCons 1
Regional constraint	o/e 0.66	unconstrained · MANE · 2,198 bp · p 3.2e-07 · regional, not allelic
Overall
CADD	24.2	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

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.Pro137Gln
Coding: c.410C>A
MANE Select: NM_005214
dbSNP: rs1553657429
Type: single nucleotide variant
Location: chr2:203870886 (GRCh38)
Gene constraint: LOEUF 0.211 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 79.67 · 22 PDB
Residue 137: a β-strand; 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

autoimmune lymphoproliferative syndrome due to CTLA4 haploinsufficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Hashimoto thyroiditis systemic lupus erythematosus type 1 diabetes mellitus 12 celiac disease, susceptibility to, 3

For Autoimmune lymphoproliferative syndrome due to CTLA4 haploinsuffiency (Orphanet):

Inheritance: Autosomal dominant
Onset: Adolescent, Adult, Childhood

Similar variants

CTLA4 p.Pro137Arg Likely pathogenic ★★★ same residue
CTLA4 p.Pro137Leu Likely pathogenic ★★★ same residue
CTLA4 p.Pro137= Likely benign ★ same residue
CTLA4 p.Arg51Ter Pathogenic ★★★ same condition
CTLA4 p.Arg75Trp Pathogenic ★★★ ⚠ same condition
CTLA4 p.Asp153Asn Pathogenic ★★★ ⚠ same condition
CTLA4 p.Cys35Ter Pathogenic ★★★ same condition
CTLA4 p.Pro136Ala 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/ctla4-p-pro137gln (accessed [today's date]).

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