Is ACSL6 p.Ile566= (c.1698C>T) pathogenic?

ACSL6 p.Ile566= (c.1698C>T) is classified Benign in ACSL6 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-10-28). Rare (popmax 0.632%, afr); Associated with ACSL6-related disorder.

What condition is associated with ACSL6 p.Ile566= (c.1698C>T)?

ACSL6 p.Ile566= (c.1698C>T) is associated with ACSL6-related disorder (ClinVar).

How common is ACSL6 p.Ile566= (c.1698C>T) in the general population?

ACSL6 p.Ile566= (c.1698C>T) is rare (popmax 0.632%, afr) (gnomAD).

ACSL6 p.Ile566=

c.1698C>T · rs73264077 · VCV3039632

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

rare (popmax 0.632%, afr)

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 -1.5	GERP -5.5
Overall
CADD	3.646	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.632% African / African-American · 474/75,024 alleles

Filtering AF 0.585% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.566%

Overall 0.0342% 552/1,614,118 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.632%	158
Middle Eastern	0.0827%	1,209
Admixed American	0.0483%	2,070
Remaining individualsnot grpmax-eligible	0.04%	2,500
East Asian	0.00891%	11,220
European (non-Finnish)	0.00127%	78,667

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.Ile566=
Coding: c.1698C>T
MANE Select: NM_001009185
dbSNP: rs73264077
Type: single nucleotide variant
Location: chr5:131966431 (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.Thr3= Likely 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-ile566 (accessed [today's date]).

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