Is ACOX2 p.Asn644= (c.1932C>T) pathogenic?

ACOX2 p.Asn644= (c.1932C>T) is classified Likely benign in ACOX2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2023-10-20). Ultra-rare (popmax 0.0121%, sas); Associated with ACOX2-related disorder.

What condition is associated with ACOX2 p.Asn644= (c.1932C>T)?

ACOX2 p.Asn644= (c.1932C>T) is associated with ACOX2-related disorder (ClinVar).

How common is ACOX2 p.Asn644= (c.1932C>T) in the general population?

ACOX2 p.Asn644= (c.1932C>T) is ultra-rare (popmax 0.0121%, sas) (gnomAD).

ACOX2 p.Asn644=

c.1932C>T · rs573721661 · VCV3036929

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0121%, sas)

Conditions

ACOX2-related disorder

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 -0.027	GERP -4.7, phastCons 0.014
Overall
CADD	5.91	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0121% South Asian · 11/91,090 alleles

Filtering AF 0.00676% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00522%

Overall 0.0013% 21/1,614,182 alleles · ultra-rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.0121%	8,281
Remaining individualsnot grpmax-eligible	0.0064%	15,627
East Asian	0.00223%	44,876
Admixed American	0.00167%	60,026
African / African-American	0.00133%	75,064
European (non-Finnish)	0.000254%	393,340

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: ACOX2
Protein: p.Asn644=
Coding: c.1932C>T
MANE Select: NM_003500
dbSNP: rs573721661
Type: single nucleotide variant
Location: chr3:58508944 (GRCh38)
Gene constraint: LOEUF 0.914 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 94.49
Residue 644: a UniProt-annotated variant site (in cbas6; patient liver samples show absence of the protein; complete loss of fatty acid beta-oxidation activity)

Full ACOX2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

ACOX2-related disorder

Similar variants

ACOX2 p.Arg329Gln Uncertain significance ★★ ⚠ same condition
ACOX2 p.Gln146Ter Uncertain significance ★ same condition
ACOX2 p.Ala395Val Uncertain significance ⚠ same condition
ACOX2 p.Lys512Asn Uncertain significance ⚠ same condition
ACOX2 p.Thr465Met Uncertain significance ⚠ same condition
ACOX2 p.Val8Glu Uncertain significance ⚠ same condition
ACOX2 c.1156-3C>T Likely benign same condition
ACOX2 c.324-3C>T Likely benign 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/acox2-p-asn644 (accessed [today's date]).

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