ABCA12 p.Ser1850Pro
c.5548T>C · rs151083083 · VCV334234
Computational evidence
| Protein change | ||
| AlphaMissense | 0.3942 | ambiguous |
|---|---|---|
| REVEL | 0.584 | indeterminate |
| SaProt | LLR -6.18 | tolerated |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 6.1 | GERP 2.4, phastCons 1 |
| Regional constraint | o/e 0.88 | unconstrained · MANE · 85 kb · p 1.7e-09 · regional, not allelic |
| Overall | ||
| CADD | 24.8 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0223% | 4,486 |
| European (non-Finnish) | 0.011% | 9,076 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,624 |
| African / African-American | 0.00133% | 75,036 |
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
- ABCA12
- Protein
- p.Ser1850Pro
- Coding
- c.5548T>C
- MANE Select
- NM_173076
- dbSNP
- rs151083083
- Type
- single nucleotide variant
- Location
- chr2:214973963 (GRCh38)
- Gene constraint
- LOEUF 0.582 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 68.32
- Residue 1850
- a UniProt-annotated variant site (in arci4b)
Similar variants
- ABCA12 c.985+1G>A Likely pathogenic ★★ same condition
- ABCA12 p.Arg1297Ter Pathogenic ★★ same condition
- ABCA12 p.Arg1515Ter Pathogenic ★★ same condition
- ABCA12 p.Arg1950Ter Pathogenic ★★ same condition
- ABCA12 p.Arg1960Ter Likely pathogenic ★★ same condition
- ABCA12 p.Arg2204Ter Pathogenic ★★ same condition
- ABCA12 p.Arg2426Gln Likely pathogenic ★★ ⚠ same condition
- ABCA12 p.Arg2482Ter 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/abca12-p-ser1850pro (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown