ABCD1 p.Cys476Ter
c.1428C>A · VCV3340680
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 5 of 10 |
| REVEL | 0.209 | benign-leaning |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.46 | GERP -2.7, phastCons 0.14 |
| Overall | ||
| CADD | 32.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- ABCD1
- Protein
- p.Cys476Ter
- Coding
- c.1428C>A
- MANE Select
- NM_000033
- Type
- single nucleotide variant
- Location
- chrX:153737191 (GRCh38)
- Structure
- AlphaFold pLDDT 81.58 · 14 PDB
- Residue 476
- a β-strand; the abc transporter domain
Similar variants
- ABCD1 p.Cys476= Conflicting classifications of pathogenicity ★ same residue
- ABCD1 p.Cys476Arg Uncertain significance ★ ⚠ same residue
- ABCD1 c.1635-2A>G Pathogenic ★★ same type
- ABCD1 c.1781-1G>C Pathogenic ★★ same type
- ABCD1 c.1781-1G>T Pathogenic/Likely pathogenic ★★ same type
- ABCD1 c.1866-10G>A Pathogenic/Likely pathogenic ★★ same type
- ABCD1 c.1866-1G>C Likely pathogenic ★★ same type
- ABCD1 c.1866-2A>T 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-cys476ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown