ABCA12 p.Lys407fs
c.1221del · VCV3646751
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 11 of 53 |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 1.1 | GERP 2.3, phastCons 0.47 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- ABCA12
- Protein
- p.Lys407fs
- Coding
- c.1221del
- MANE Select
- NM_173076
- Type
- Deletion
- Location
- chr2:215025739 (GRCh38)
- Gene constraint
- LOEUF 0.582 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.32
Similar variants
- ABCA12 p.Lys407= Likely benign ★ same residue
- ABCA12 p.Asn528fs Pathogenic/Likely pathogenic ★★ same type
- ABCA12 p.Ile1128fs Pathogenic/Likely pathogenic ★★ same type
- ABCA12 p.Phe2286fs Pathogenic ★★ same type
- ABCA12 p.Val2442fs Pathogenic ★★ same type
- ABCA12 c.2683+2del Likely pathogenic ★ same type
- ABCA12 c.5469_5472del Pathogenic ★ same type
- ABCA12 c.6962+2del Likely pathogenic ★ 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/abca12-p-lys407fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown