ABCC1 p.Phe666=
c.1998C>T · rs757045428 · VCV750105
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00666%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.23 | acceptor gain · deltas |
|---|---|---|
| Pangolin | Δ0.20 | gain · loss 0.05 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 3.2 | GERP -0.44, phastCons 1 |
| Overall | ||
| CADD | 16.38 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00666%
Admixed American · 4/60,016 alleles
Filtering AF
0.00226%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00135%
Overall
0.000372%
6/1,614,076 alleles · very rare
exomes 6/1,461,738 · genomes 0/152,338 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00666% | 15,004 |
| East Asian | 0.00223% | 44,880 |
| South Asian | 0.0011% | 91,076 |
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
- ABCC1
- Protein
- p.Phe666=
- Coding
- c.1998C>T
- MANE Select
- NM_004996
- dbSNP
- rs757045428
- Type
- single nucleotide variant
- Location
- chr16:16079361 (GRCh38)
- Gene constraint
- LOEUF 0.564 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.01 · 5 PDB
- Residue 666
- a β-strand; the abc transporter 1 domain
Similar variants
- ABCC1 p.Thr1464Met Uncertain significance ★★ ⚠ same type
- ABCC1 c.1381-5C>G Benign ★★ same type
- ABCC1 p.Ala1260= Benign ★★ same type
- ABCC1 p.Ala1406= Benign ★★ same type
- ABCC1 p.Arg433Ser Benign ★★ same type
- ABCC1 p.Asp637= Likely benign ★★ same type
- ABCC1 p.Gly762= Benign/Likely benign ★★ same type
- ABCC1 p.Gly885= Benign ★★ 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/abcc1-p-phe666 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown