Is AIP p.Thr231= (c.693G>A) pathogenic?

AIP p.Thr231= (c.693G>A) is classified Benign/Likely benign in AIP (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-02-01). Rare (popmax 0.127%, afr); Associated with hereditary neoplastic syndrome.

What condition is associated with AIP p.Thr231= (c.693G>A)?

AIP p.Thr231= (c.693G>A) is associated with hereditary neoplastic syndrome (ClinVar).

How common is AIP p.Thr231= (c.693G>A) in the general population?

AIP p.Thr231= (c.693G>A) is rare (popmax 0.127%, afr) (gnomAD).

AIP p.Thr231=

c.693G>A · rs141715817 · VCV734010

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

rare (popmax 0.127%, afr)

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -12	GERP -3.6
Overall
CADD	0.206	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.127% African / African-American · 95/75,030 alleles

Filtering AF 0.106% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0983%

Overall 0.00707% 114/1,612,292 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.127%	790
Remaining individualsnot grpmax-eligible	0.0128%	7,811
Admixed American	0.00833%	12,002
European (non-Finnish)	0.000509%	196,630

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.Thr231=
Coding: c.693G>A
MANE Select: NM_017900 · reported on NM_003977
dbSNP: rs141715817
Type: single nucleotide variant
Location: chr11:67490363 (GRCh38)
Structure: AlphaFold pLDDT 70.14 · 81 PDB

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.Thr231Met Conflicting classifications of pathogenicity ★ ⚠ 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
AIP p.Gln14Ter Pathogenic ★★ same condition
AIP p.Gln217Ter 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-thr231 (accessed [today's date]).

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