Is AIP p.Arg39Gly (c.115C>G) pathogenic?

AIP p.Arg39Gly (c.115C>G) is classified Uncertain significance in AIP (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-10-23). AlphaMissense: ambiguous (0.4445); Absent from gnomAD v4.1; Associated with hereditary neoplastic syndrome.

What condition is associated with AIP p.Arg39Gly (c.115C>G)?

AIP p.Arg39Gly (c.115C>G) is associated with hereditary neoplastic syndrome (ClinVar).

How common is AIP p.Arg39Gly (c.115C>G) in the general population?

AIP p.Arg39Gly (c.115C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about AIP p.Arg39Gly (c.115C>G)?

AlphaMissense predicts ambiguous (score 0.4445) — an in-silico prediction, not a clinical call.

AIP p.Arg39Gly

c.115C>G · rs781366620 · VCV1001466

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

ambiguous

0.4445 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/2 damaging

REVEL, SaProt · AlphaMissense no call

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
AlphaMissense	0.4445	ambiguous
REVEL	0.725	pathogenic-leaning
SaProt	LLR -13.53	damaging
⇒ REVEL and SaProt both call this damaging; AlphaMissense makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4	GERP 1.8, phastCons 1
Overall
CADD	24.1	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: AIP
Protein: p.Arg39Gly
Coding: c.115C>G
MANE Select: NM_003977
dbSNP: rs781366620
Type: single nucleotide variant
Location: chr11:67487021 (GRCh38)
Gene constraint: LOEUF 0.626 · pLI 0.28 (gnomAD)
Structure: AlphaFold pLDDT 91.09 · 5 PDB
Residue 39: the ppiase fkbp-type domain; a β-strand

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

Disease context

hereditary neoplastic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

AIP p.Arg39Gln Uncertain significance ★★ ⚠ same residue
AIP p.Arg39Trp Uncertain significance ★★ ⚠ same residue
AIP p.Arg39= Likely benign ★ same residue
AIP p.Arg271Trp Pathogenic/Likely pathogenic ★★ same condition
AIP p.Arg304Ter Pathogenic ★★ same condition
AIP p.Arg81Ter Pathogenic ★★ same condition
AIP p.Cys238Tyr Likely pathogenic ★★ same condition
AIP p.Gln126Ter 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/aip-p-arg39gly (accessed [today's date]).

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