ABCA5 p.Val1507=
c.4521G>A · rs199848425 · VCV3042879
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0936%, eas)
Conditions
1
ABCA5-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.77 | donor gain · deltas |
|---|---|---|
| Pangolin | Δ0.60 | gain · loss 0.17 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP -1.4 | GERP -2.4 |
| Overall | ||
| CADD | 17.14 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0936%
East Asian · 42/44,862 alleles
Filtering AF
0.0712%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0632%
Overall
0.00328%
53/1,613,940 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0936% | 1,068 |
| African / African-American | 0.00666% | 15,007 |
| Admixed American | 0.00334% | 29,981 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,244 |
| European (non-Finnish) | 0.000169% | 589,981 |
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
- ABCA5
- Protein
- p.Val1507=
- Coding
- c.4521G>A
- MANE Select
- NM_172232
- dbSNP
- rs199848425
- Type
- single nucleotide variant
- Location
- chr17:69251761 (GRCh38)
- Gene constraint
- LOEUF 0.97 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.12
- Residue 1507
- the abc transporter 2 domain
Disease context
ABCA5-related disorder
Similar variants
- ABCA5 c.4415+3G>A Likely benign same condition
- ABCA5 c.788+8A>C Likely benign same condition
- ABCA5 p.Ala1444= Likely benign same condition
- ABCA5 p.Ala178Thr Benign ⚠ same condition
- ABCA5 p.Arg555= Likely benign same condition
- ABCA5 p.Gln484Arg Benign same condition
- ABCA5 p.Leu1131= Benign same condition
- ABCA5 p.Leu1183= Benign 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/abca5-p-val1507 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown