ABCD1 p.Ile657fs
c.1966_1967dup · rs2148399303 · VCV1322475
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | escapes | premature termination codon within the last 50 nt of the penultimate exon (9 of 10, 29 nt from its 3' end) — the truncated protein is likely expressed. PVS1 input, not an applied code |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 2.8 | GERP -3.1, phastCons 1 |
| Region caveats | ||
| Repeat context | seg dup | · reads may not map uniquely · confidence, not pathogenicity |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- ABCD1
- Protein
- p.Ile657fs
- Coding
- c.1966_1967dup
- MANE Select
- NM_000033
- dbSNP
- rs2148399303
- Type
- Microsatellite
- Location
- chrX:153743317 (GRCh38)
- Structure
- AlphaFold pLDDT 81.58 · 14 PDB
- Residue 657
- a UniProt-annotated variant site (in ald; cald-type); a β-strand; the abc transporter domain
Similar variants
- ABCD1 p.Ile657del Pathogenic/Likely pathogenic ★★ same residue
- ABCD1 p.Glu292del Pathogenic/Likely pathogenic ★★ same type
- ABCD1 p.Lys373del Uncertain significance ★★ same type
- ABCD1 p.Leu139del Likely pathogenic ★ same type
- ABCD1 p.Leu197fs Pathogenic ★ same type
- ABCD1 p.Leu670fs Likely pathogenic ★ same type
- ABCD1 p.Pro143fs Pathogenic ★ same type
- ABCD1 p.Val251del 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/abcd1-p-ile657fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown