ABCC9 p.Ser404=
c.1212C>T · rs376726505 · VCV227157
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0331%, mid)
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 0.79 | GERP 0.9, phastCons 1 |
| Overall | ||
| CADD | 7.323 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0331%
Middle Eastern · 2/6,050 alleles
Filtering AF
0.0142%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0113%
Overall
0.00304%
49/1,609,976 alleles · ultra-rare
exomes 43/1,459,456 · genomes 6/150,520 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0331% | 3,025 |
| Admixed American | 0.0235% | 4,263 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,799 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00678% | 14,757 |
| East Asian | 0.00223% | 44,794 |
| European (non-Finnish) | 0.0017% | 58,908 |
| African / African-American | 0.00134% | 74,436 |
| South Asian | 0.0011% | 90,928 |
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.Ser404=
- Coding
- c.1212C>T
- MANE Select
- NM_020297
- dbSNP
- rs376726505
- Type
- single nucleotide variant
- Location
- chr12:21910265 (GRCh38)
- Gene constraint
- LOEUF 0.557 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.72
- Residue 404
- the abc transmembrane type-1 1 domain
Similar variants
- 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
- ABCC9 p.Val1266Met 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-ser404 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown