ABCD1 p.Ser485=
c.1455A>C · rs150878397 · VCV588489
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 7 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0695%, amr)
Conditions
2
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.032 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -6.1 | GERP -3.1 |
| Overall | ||
| CADD | 0.048 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0695%
Admixed American · 32/46,055 alleles
Filtering AF
0.0506%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0441%
Overall
0.00454%
55/1,210,690 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0695% | 1,439 |
| Remaining individualsnot grpmax-eligible | 0.0294% | 3,402 |
| Middle Eastern | 0.023% | 4,346 |
| Finnishnot grpmax-eligible | 0.00217% | 46,118 |
| European (non-Finnish) | 0.000782% | 127,908 |
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.Ser485=
- Coding
- c.1455A>C
- MANE Select
- NM_000033
- dbSNP
- rs150878397
- Type
- single nucleotide variant
- Location
- chrX:153737218 (GRCh38)
- Structure
- AlphaFold pLDDT 81.58 · 14 PDB
- Residue 485
- a β-strand; the abc transporter domain
Similar variants
- ABCD1 p.Ser485Ter Pathogenic ★ same residue
- 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
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-ser485 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown