ABCC1 p.Ser465=
c.1395C>T · VCV4928681
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.024%, afr)
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 -20 | GERP -3.4 |
| Overall | ||
| CADD | 0.249 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.024%
African / African-American · 18/74,906 alleles
Filtering AF
0.0155%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0128%
Overall
0.00167%
27/1,613,988 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.024% | 4,161 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,490 |
| South Asian | 0.0011% | 91,078 |
| European (non-Finnish) | 0.000593% | 168,573 |
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.Ser465=
- Coding
- c.1395C>T
- MANE Select
- NM_004996
- Type
- single nucleotide variant
- Location
- chr16:16052738 (GRCh38)
- Gene constraint
- LOEUF 0.564 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.01 · 5 PDB
- Residue 465
- the abc transmembrane type-1 1 domain
Similar variants
- ABCC1 p.Ser465Cys Uncertain significance ★ ⚠ same residue
- 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
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-ser465 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown