ACSF3 p.Leu2Pro
c.5_6inv · VCV1083859
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
Conditions
1
combined malonic and methylmalonic acidemia
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -15 | GERP -3.3 |
| Regional constraint | o/e 1.22 | unconstrained · MANE · 54 kb · p 2.3e-09 · regional, not allelic |
Variant & gene context
- Gene
- ACSF3
- Protein
- p.Leu2Pro
- Coding
- c.5_6inv
- MANE Select
- NM_001243279
- Type
- Inversion
- Location
- chr16:89100686 (GRCh38)
- Gene constraint
- LOEUF 1.715 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 86.58
- Residue 2
- a UniProt-annotated variant site (in)
Disease context
combined malonic and methylmalonic acidemia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Combined malonic and methylmalonic acidemia (Orphanet):
- Inheritance
- Autosomal dominant, Autosomal recessive
- Onset
- All ages
- Prevalence
- 1-9 / 100 000 (United States)
Similar variants
- ACSF3 c.1366+1G>A Likely pathogenic ★★ same condition
- ACSF3 c.1501+1G>A Likely pathogenic ★★ same condition
- ACSF3 c.1501+1G>T Likely pathogenic ★★ same condition
- ACSF3 c.1502-2A>G Pathogenic/Likely pathogenic ★★ same condition
- ACSF3 c.1613+1G>A Pathogenic/Likely pathogenic ★★ same condition
- ACSF3 c.666+1G>A Pathogenic/Likely pathogenic ★★ same condition
- ACSF3 c.666+1G>T Likely pathogenic ★★ same condition
- ACSF3 c.667-2A>G Likely pathogenic ★★ 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/acsf3-p-leu2pro (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown