Is AEBP2 p.Thr137Ile (c.410C>T) pathogenic?

AEBP2 p.Thr137Ile (c.410C>T) is classified Uncertain significance in AEBP2 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-12-25). AlphaMissense: likely benign (0.1535); Ultra-rare (popmax 0.0528%, sas).

How common is AEBP2 p.Thr137Ile (c.410C>T) in the general population?

AEBP2 p.Thr137Ile (c.410C>T) is ultra-rare (popmax 0.0528%, sas) (gnomAD).

What do computational predictors say about AEBP2 p.Thr137Ile (c.410C>T)?

AlphaMissense predicts likely benign (score 0.1535) — an in-silico prediction, not a clinical call.

AEBP2 p.Thr137Ile

c.410C>T · VCV3839534

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1535 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0528%, sas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1535	likely benign
REVEL	0.119	moderately benign-leaning
SaProt	LLR -7.34	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.1	GERP 0.27, phastCons 1
Regional constraint	o/e 1.15	unconstrained · MANE · 659 bp · p 0.0074 · regional, not allelic
Overall
CADD	23.0	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 0.0528% South Asian · 43/81,408 alleles

Filtering AF 0.0403% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0358%

Overall 0.00345% 52/1,505,908 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0528%	1,893
African / African-American	0.00433%	23,069
Remaining individualsnot grpmax-eligible	0.00341%	29,311
European (non-Finnish)	0.000353%	283,423

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: AEBP2
Protein: p.Thr137Ile
Coding: c.410C>T
MANE Select: NM_153207
Type: single nucleotide variant
Location: chr12:19440109 (GRCh38)
Gene constraint: LOEUF 0.461 · pLI 0.99 (gnomAD)
Structure: AlphaFold pLDDT 63.62 · 21 PDB
Residue 137: the 'disordered' region

Full AEBP2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

AEBP2 p.Ala198Pro Uncertain significance ★ ⚠ same type
AEBP2 p.Ala33Pro Uncertain significance ★ ⚠ same type
AEBP2 p.Ala4Ser Uncertain significance ★ ⚠ same type
AEBP2 p.Arg138Ser Uncertain significance ★ ⚠ same type
AEBP2 p.Arg16Pro Uncertain significance ★ ⚠ same type
AEBP2 p.Asn273Thr Uncertain significance ★ ⚠ same type
AEBP2 p.Asn336Asp Uncertain significance ★ ⚠ same type
AEBP2 p.Asn336Ser Uncertain significance ★ ⚠ 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/aebp2-p-thr137ile (accessed [today's date]).

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