Is AIP p.Arg307Gln (c.920G>A) pathogenic?

AIP p.Arg307Gln (c.920G>A) is classified Uncertain significance in AIP (ClinVar, Single submitter, 1 submitter; last evaluated 2026-01-21). AlphaMissense: likely benign (0.0893); Ultra-rare (popmax 0.0417%, sas).

How common is AIP p.Arg307Gln (c.920G>A) in the general population?

AIP p.Arg307Gln (c.920G>A) is ultra-rare (popmax 0.0417%, sas) (gnomAD).

What do computational predictors say about AIP p.Arg307Gln (c.920G>A)?

AlphaMissense predicts likely benign (score 0.0893) — an in-silico prediction, not a clinical call.

AIP p.Arg307Gln

c.920G>A · rs4930199 · VCV837193

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0893 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0417%, sas)

Missense predictors

0/2 damaging

AlphaMissense, SaProt

Computational evidence

Protein change
AlphaMissense	0.0893	likely benign
SaProt	LLR -6.76	tolerated
⇒ AlphaMissense and SaProt both call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 5.9	GERP 2, phastCons 1
Overall
CADD	18.24	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0417% South Asian · 38/91,048 alleles

Filtering AF 0.0312% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0276%

Overall 0.00589% 95/1,612,442 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0417%	2,396
African / African-American	0.0306%	3,263
Admixed American	0.015%	6,662
Remaining individualsnot grpmax-eligible	0.00961%	10,409
Finnishnot grpmax-eligible	0.0016%	62,672
European (non-Finnish)	0.00153%	65,547

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: AIP
Protein: p.Arg307Gln
Coding: c.920G>A
MANE Select: NM_017900 · reported on NM_003977
dbSNP: rs4930199
Type: single nucleotide variant
Location: chr11:67490920 (GRCh38)
Structure: AlphaFold pLDDT 70.14 · 81 PDB

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

Similar variants

AIP p.Arg307Trp Uncertain significance ★★ ⚠ same residue
AIP p.Arg307= Uncertain significance ★ same residue
AIP p.Arg307Gly Uncertain significance ★ ⚠ same residue
AIP p.Arg307Pro Uncertain significance ★ ⚠ same residue
AIP p.Arg307fs Conflicting classifications of pathogenicity ★ same residue
AIP p.Arg271Trp Pathogenic/Likely pathogenic ★★ same type
AIP p.Arg304Ter Pathogenic ★★ same type
AIP p.Arg81Ter 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/aip-p-arg307gln (accessed [today's date]).

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