Is ACAD11 p.Leu25= (c.73C>T) pathogenic?

ACAD11 p.Leu25= (c.73C>T) is classified Likely benign in ACAD11 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-01). Very rare (popmax 0.00268%, afr).

How common is ACAD11 p.Leu25= (c.73C>T) in the general population?

ACAD11 p.Leu25= (c.73C>T) is very rare (popmax 0.00268%, afr) (gnomAD).

ACAD11 p.Leu25=

c.73C>T · VCV3898485

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00268%, afr)

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 3.8	GERP -0.67, phastCons 1
Overall
CADD	11.7	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00268% African / African-American · 2/74,736 alleles

Filtering AF 0.000444% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000211%

Overall 0.000621% 10/1,611,458 alleles · very rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00268%	37,368
European (non-Finnish)	0.000679%	147,352

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: ACAD11
Protein: p.Leu25=
Coding: c.73C>T
MANE Select: NM_032169
Type: single nucleotide variant
Location: chr3:132659679 (GRCh38)
Gene constraint: LOEUF 1.01 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 91.00 · 1 PDB

Full ACAD11 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ACAD11 p.Ala191Thr Uncertain significance ★ ⚠ same type
ACAD11 p.Ala516Val Uncertain significance ★ ⚠ same type
ACAD11 p.Ala550Pro Uncertain significance ★ ⚠ same type
ACAD11 p.Ala646Thr Uncertain significance ★ ⚠ same type
ACAD11 p.Ala680Gly Uncertain significance ★ ⚠ same type
ACAD11 p.Ala725Pro Uncertain significance ★ ⚠ same type
ACAD11 p.Ala741Val Uncertain significance ★ ⚠ same type
ACAD11 p.Ala765Thr 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/acad11-p-leu25 (accessed [today's date]).

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