ABCD1 p.Cys511Ter
c.1533C>A · VCV3338821
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 6 of 10 |
| REVEL | 0.328 | indeterminate |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -9.6 | GERP -3.7 |
| Overall | ||
| CADD | 23.8 | 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.Cys511Ter
- Coding
- c.1533C>A
- MANE Select
- NM_000033
- Type
- single nucleotide variant
- Location
- chrX:153740136 (GRCh38)
- Structure
- AlphaFold pLDDT 81.58 · 14 PDB
- Residue 511
- a binding site; a β-strand; the abc transporter domain
Similar variants
- ABCD1 p.Cys511Trp Conflicting classifications of pathogenicity ★ ⚠ same residue
- ABCD1 p.Cys511Tyr Conflicting classifications of pathogenicity ★ ⚠ same residue
- ABCD1 p.Cys511= Likely benign ★ same residue
- ABCD1 p.Cys511_Gly512del Pathogenic ★ same residue
- ABCD1 p.Cys511fs Pathogenic ★ 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
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-cys511ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown