ABCC9 p.Phe1463=
c.4389T>C · rs530506599 · VCV676414
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.078%, eas)
Conditions
2
Cardiovascular phenotype
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 -0.9 | GERP -3.7 |
| Overall | ||
| CADD | 6.499 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.078%
East Asian · 35/44,870 alleles
Filtering AF
0.0576%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0506%
Overall
0.00353%
57/1,614,040 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.078% | 1,282 |
| Middle Eastern | 0.0165% | 6,062 |
| African / African-American | 0.00666% | 15,012 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,835 |
| South Asian | 0.0022% | 45,543 |
| European (non-Finnish) | 0.000932% | 107,263 |
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
- ABCC9
- Protein
- p.Phe1463=
- Coding
- c.4389T>C
- MANE Select
- NM_020297
- dbSNP
- rs530506599
- Type
- single nucleotide variant
- Location
- chr12:21807406 (GRCh38)
- Gene constraint
- LOEUF 0.557 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.72
- Residue 1463
- the abc transporter 2 domain
Similar variants
- ABCC9 p.Phe1463fs Uncertain significance ★ same residue
- ABCC9 c.2506-1G>A Pathogenic/Likely pathogenic ★★ same condition
- ABCC9 p.Arg1116Cys Pathogenic/Likely pathogenic ★★ ⚠ same condition
- ABCC9 p.Arg1116His Pathogenic ★★ ⚠ same condition
- ABCC9 p.Arg1154Gln Pathogenic ★★ same condition
- ABCC9 p.Arg1154Trp Pathogenic/Likely pathogenic ★★ same condition
- ABCC9 p.Gln852Ter Pathogenic/Likely pathogenic ★★ same condition
- ABCC9 p.Thr1202Met Pathogenic/Likely pathogenic ★★ ⚠ 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/abcc9-p-phe1463 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown