ABCB5 p.Ser553=
c.1659T>G · rs78859324 · VCV2657334
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.985%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.53 | GERP -3.9, phastCons 1 |
| Overall | ||
| CADD | 5.63 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.985%
African / African-American · 739/75,046 alleles
Filtering AF
0.926%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.902%
Overall
0.0503%
812/1,614,194 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.985% | 102 |
| Remaining individualsnot grpmax-eligible | 0.056% | 1,786 |
| Admixed American | 0.0417% | 2,401 |
| Middle Eastern | 0.0165% | 6,062 |
| South Asian | 0.0022% | 45,541 |
| European (non-Finnish) | 0.000847% | 118,003 |
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
- ABCB5
- Protein
- p.Ser553=
- Coding
- c.1659T>G
- MANE Select
- NM_001163941
- dbSNP
- rs78859324
- Type
- single nucleotide variant
- Location
- chr7:20658628 (GRCh38)
- Gene constraint
- LOEUF 1.178 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.01
- Residue 553
- the abc transporter 1 domain
Similar variants
- ABCB5 p.Ala350Thr Likely benign ★★ ⚠ same type
- ABCB5 p.Val1209Ala Likely benign ★★ ⚠ same type
- ABCB5 p.Ala1112Thr Uncertain significance ★ ⚠ same type
- ABCB5 p.Ala1154Gly Uncertain significance ★ ⚠ same type
- ABCB5 p.Ala221Val Uncertain significance ★ ⚠ same type
- ABCB5 p.Ala223Ser Uncertain significance ★ ⚠ same type
- ABCB5 p.Ala327Thr Uncertain significance ★ ⚠ same type
- ABCB5 p.Ala501Glu 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/abcb5-p-ser553 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown