Is AEN p.Arg231Trp (c.691C>T) pathogenic?

AEN p.Arg231Trp (c.691C>T) is classified Uncertain significance in AEN (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-22). AlphaMissense: likely benign (0.1781); Very rare (popmax 0.00333%, amr).

How common is AEN p.Arg231Trp (c.691C>T) in the general population?

AEN p.Arg231Trp (c.691C>T) is very rare (popmax 0.00333%, amr) (gnomAD).

What do computational predictors say about AEN p.Arg231Trp (c.691C>T)?

AlphaMissense predicts likely benign (score 0.1781) — an in-silico prediction, not a clinical call.

AEN p.Arg231Trp

c.691C>T · VCV3503107

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1781 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00333%, amr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1781	likely benign
REVEL	0.214	benign-leaning
SaProt	LLR -9.97	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 3.3	GERP -0.89, phastCons 1
Regional constraint	o/e 1.06	unconstrained · MANE · 4,081 bp · p 0.21 · regional, not allelic
Overall
CADD	25.1	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 0.00333% Admixed American · 2/60,010 alleles

Filtering AF 0.000553% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000312%

Overall 0.000805% 13/1,614,010 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00333%	30,005
Remaining individualsnot grpmax-eligible	0.0016%	62,486
European (non-Finnish)	0.000847%	118,002

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: AEN
Protein: p.Arg231Trp
Coding: c.691C>T
MANE Select: NM_022767
Type: single nucleotide variant
Location: chr15:88629376 (GRCh38)
Gene constraint: LOEUF 1.666 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 75.19
Residue 231: the exonuclease domain

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

Similar variants

AEN p.Ala10Ser Uncertain significance ★ ⚠ same type
AEN p.Ala112Ser Uncertain significance ★ ⚠ same type
AEN p.Ala194Thr Uncertain significance ★ ⚠ same type
AEN p.Ala201Val Uncertain significance ★ ⚠ same type
AEN p.Ala45Ser Uncertain significance ★ ⚠ same type
AEN p.Arg125Trp Uncertain significance ★ ⚠ same type
AEN p.Arg131Cys Uncertain significance ★ ⚠ same type
AEN p.Arg131His 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/aen-p-arg231trp (accessed [today's date]).

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