ABCD4 p.Leu41=
c.123G>A · rs1595083188 · VCV737146
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.31 | donor loss, 34 bp away · masked 0 · deltas |
|---|---|---|
| Pangolin | Δ0.24 | loss · gain 0.01 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 0.33 | GERP 0.44, phastCons 0.99 |
| Overall | ||
| CADD | 2.763 | PHRED · no single calibrated threshold — expert panels disagree |
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
- ABCD4
- Protein
- p.Leu41=
- Coding
- c.123G>A
- MANE Select
- NM_005050
- dbSNP
- rs1595083188
- Type
- single nucleotide variant
- Location
- chr14:74300184 (GRCh38)
- Gene constraint
- LOEUF 0.772 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.18 · 4 PDB
- Residue 41
- the abc transmembrane type-1 domain
Similar variants
- ABCD4 c.542+1G>T Pathogenic ★★ same type
- ABCD4 p.Arg432Gln Likely pathogenic ★★ same type
- ABCD4 p.Asn141Lys Pathogenic/Likely pathogenic ★★ same type
- ABCD4 p.Gln530Ter Pathogenic/Likely pathogenic ★★ same type
- ABCD4 p.Tyr176Ter Pathogenic/Likely pathogenic ★★ same type
- ABCD4 c.1028+5G>A Uncertain significance ★★ same type
- ABCD4 c.425+6C>T Uncertain significance ★★ same type
- ABCD4 c.719+6T>C Uncertain significance ★★ 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/abcd4-p-leu41 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown