Is ACSL6 p.Thr3= (c.9C>T) pathogenic?

ACSL6 p.Thr3= (c.9C>T) is classified Likely benign in ACSL6 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-10-28). Ultra-rare (popmax 0.0829%, amr); Associated with ACSL6-related disorder.

What condition is associated with ACSL6 p.Thr3= (c.9C>T)?

ACSL6 p.Thr3= (c.9C>T) is associated with ACSL6-related disorder (ClinVar).

How common is ACSL6 p.Thr3= (c.9C>T) in the general population?

ACSL6 p.Thr3= (c.9C>T) is ultra-rare (popmax 0.0829%, amr) (gnomAD).

ACSL6 p.Thr3=

c.9C>T · rs145839757 · VCV3040468

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0829%, amr)

Conditions

ACSL6-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 4	GERP 1.1, phastCons 1
Overall
CADD	15.81	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0829% Admixed American · 49/59,080 alleles

Filtering AF 0.0644% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0579%

Overall 0.0201% 321/1,599,938 alleles · ultra-rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.0829%	1,206
Middle Eastern	0.0666%	1,500
Remaining individualsnot grpmax-eligible	0.0356%	2,807
African / African-American	0.0218%	4,593
European (non-Finnish)	0.0196%	5,103

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: ACSL6
Protein: p.Thr3=
Coding: c.9C>T
MANE Select: NM_001009185
dbSNP: rs145839757
Type: single nucleotide variant
Location: chr5:132011545 (GRCh38)
Gene constraint: LOEUF 0.584 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 90.15

Full ACSL6 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

ACSL6-related disorder

Similar variants

ACSL6 p.Lys668Glu Uncertain significance ★ ⚠ same condition
ACSL6 p.Val223Met Uncertain significance ★ ⚠ same condition
ACSL6 c.865-8C>G Benign same condition
ACSL6 p.Ala152= Likely benign same condition
ACSL6 p.Arg412Cys Likely benign ⚠ same condition
ACSL6 p.Glu17= Likely benign same condition
ACSL6 p.Ile566= Benign same condition
ACSL6 p.Thr651Ala 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/acsl6-p-thr3 (accessed [today's date]).

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