ABCD1 p.Arg545=
c.1635G>A · rs1557054842 · VCV2178535
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00434%, amr)
Conditions
2
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.177 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.32 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP 5.5 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 15.03 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00434%
Admixed American · 2/46,072 alleles
Filtering AF
0.00072%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000269%
Overall
0.000165%
2/1,210,278 alleles · very rare
exomes 2/1,096,382 · genomes 0/113,896 · joint denominator
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- ABCD1
- Protein
- p.Arg545=
- Coding
- c.1635G>A
- MANE Select
- NM_000033
- dbSNP
- rs1557054842
- Type
- single nucleotide variant
- Location
- chrX:153740574 (GRCh38)
- Structure
- AlphaFold pLDDT 81.58 · 14 PDB
- Residue 545
- the abc transporter domain
Similar variants
- ABCD1 c.1635-2A>G Pathogenic ★★ same condition
- ABCD1 c.1781-1G>C Pathogenic ★★ same condition
- ABCD1 c.1781-1G>T Pathogenic/Likely pathogenic ★★ same condition
- ABCD1 c.1866-10G>A Pathogenic/Likely pathogenic ★★ same condition
- ABCD1 c.1866-1G>C Likely pathogenic ★★ same condition
- ABCD1 c.1866-2A>T Likely pathogenic ★★ same condition
- ABCD1 c.901-1G>A Pathogenic ★★ same condition
- ABCD1 c.901-5C>A 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/abcd1-p-arg545 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown