ABCB7 p.Ser386=
c.1158T>C · rs1268328600 · VCV755891
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00658%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.25 | donor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.9 | GERP -2.6, phastCons 0.99 |
| Overall | ||
| CADD | 9.186 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00658%
Admixed American · 3/45,623 alleles
Filtering AF
0.00174%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000883%
Overall
0.000331%
4/1,209,483 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00658% | 15,208 |
| European (non-Finnish) | 0.000112% | 895,063 |
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
- ABCB7
- Protein
- p.Ser386=
- Coding
- c.1158T>C
- MANE Select
- NM_001271696
- dbSNP
- rs1268328600
- Type
- single nucleotide variant
- Location
- chrX:75071558 (GRCh38)
- Structure
- AlphaFold pLDDT 78.19 · 4 PDB
- Residue 386
- the abc transmembrane type-1 domain; an α-helix
Similar variants
- ABCB7 c.1659+5T>G Uncertain significance ★★ same type
- ABCB7 c.1935+5G>C Uncertain significance ★★ same type
- ABCB7 p.Ala5Glu Uncertain significance ★★ ⚠ same type
- ABCB7 p.Arg711His Uncertain significance ★★ ⚠ same type
- ABCB7 p.Asn378Asp Uncertain significance ★★ ⚠ same type
- ABCB7 p.Asp653Asn Uncertain significance ★★ ⚠ same type
- ABCB7 p.Glu494Gln Uncertain significance ★★ ⚠ same type
- ABCB7 p.Gly197Cys 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/abcb7-p-ser386 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown