Is ACOX2 p.Arg50Cys (c.148C>T) pathogenic?

ACOX2 p.Arg50Cys (c.148C>T) is classified Uncertain significance in ACOX2 (ClinVar, Single submitter, 2 submitters; last evaluated 2025-09-24). AlphaMissense: ambiguous (0.5352); Very rare (popmax 0.01%, amr).

How common is ACOX2 p.Arg50Cys (c.148C>T) in the general population?

ACOX2 p.Arg50Cys (c.148C>T) is very rare (popmax 0.01%, amr) (gnomAD).

What do computational predictors say about ACOX2 p.Arg50Cys (c.148C>T)?

AlphaMissense predicts ambiguous (score 0.5352) — an in-silico prediction, not a clinical call.

ACOX2 p.Arg50Cys

c.148C>T · rs149911289 · VCV3029531

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

ambiguous

0.5352 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.01%, amr)

Computational evidence

Protein change
AlphaMissense	0.5352	ambiguous
REVEL	0.437	indeterminate
SaProt	LLR -13.77	damaging
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.9	GERP 0.048, phastCons 1
Regional constraint	o/e 0.95	unconstrained · MANE · 30 kb · p 0.14 · regional, not allelic
Overall
CADD	28.8	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.01% Admixed American · 6/60,002 alleles

Filtering AF 0.00428% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00295%

Overall 0.00285% 46/1,614,074 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.01%	10,000
South Asian	0.00439%	22,772
Ashkenazi Jewishnot grpmax-eligible	0.00338%	29,604
European (non-Finnish)	0.0028%	35,758
Remaining individualsnot grpmax-eligible	0.0016%	62,482
African / African-American	0.00133%	74,942

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.Arg50Cys
Coding: c.148C>T
MANE Select: NM_003500
dbSNP: rs149911289
Type: single nucleotide variant
Location: chr3:58534959 (GRCh38)
Gene constraint: LOEUF 0.914 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 94.49

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

Similar variants

ACOX2 p.Arg50His Uncertain significance ★ ⚠ same residue
ACOX2 p.Ala106Val Uncertain significance ★★ ⚠ same type
ACOX2 p.Ala48Glu Uncertain significance ★★ ⚠ same type
ACOX2 p.Arg197Gln Uncertain significance ★★ ⚠ same type
ACOX2 p.Arg197Trp Uncertain significance ★★ ⚠ same type
ACOX2 p.Arg215Trp Uncertain significance ★★ ⚠ same type
ACOX2 p.Arg318His Uncertain significance ★★ ⚠ same type
ACOX2 p.Arg323Cys 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/acox2-p-arg50cys (accessed [today's date]).

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