ABCD4 p.Gly501=
c.1503C>G · rs757278296 · VCV1335153
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0165%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| REVEL | 0.006 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | Δ0.28 | donor loss, 3 bp away · masked 0 · deltas |
| Pangolin | Δ0.21 | loss · gain 0.01 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 1.5 | GERP -1.9, phastCons 1 |
| Overall | ||
| CADD | 6.77 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0165%
Middle Eastern · 1/6,062 alleles
Overall
0.000137%
2/1,461,178 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0165% | 6,062 |
| European (non-Finnish) | 8.48e-05% | 1,179,784 |
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
- ABCD4
- Protein
- p.Gly501=
- Coding
- c.1503C>G
- MANE Select
- NM_005050
- dbSNP
- rs757278296
- Type
- single nucleotide variant
- Location
- chr14:74288719 (GRCh38)
- Gene constraint
- LOEUF 0.772 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 87.18 · 4 PDB
- Residue 501
- the abc transporter 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-gly501 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown