ABCC2 p.His1414=
c.4242C>T · rs17216296 · VCV2716629
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.044%, 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 0.83 | GERP -1.4, phastCons 1 |
| Overall | ||
| CADD | 6.251 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.044%
African / African-American · 33/75,062 alleles
Filtering AF
0.0321%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0281%
Overall
0.00254%
41/1,614,234 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.044% | 2,275 |
| Middle Eastern | 0.0165% | 6,062 |
| Admixed American | 0.00833% | 12,006 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,255 |
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
- ABCC2
- Protein
- p.His1414=
- Coding
- c.4242C>T
- MANE Select
- NM_000392
- dbSNP
- rs17216296
- Type
- single nucleotide variant
- Location
- chr10:99847056 (GRCh38)
- Gene constraint
- LOEUF 0.985 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.40 · 16 PDB
- Residue 1414
- the abc transporter 2 domain
Similar variants
- ABCC2 p.His1414Tyr Uncertain significance ★ ⚠ same residue
- ABCC2 p.His1414fs Pathogenic ★ same residue
- ABCC2 c.1031+4A>G Pathogenic/Likely pathogenic ★★ same type
- ABCC2 c.1967+1G>A Pathogenic/Likely pathogenic ★★ same type
- ABCC2 c.1968-1G>C Pathogenic/Likely pathogenic ★★ same type
- ABCC2 c.3258+1G>A Pathogenic/Likely pathogenic ★★ same type
- ABCC2 c.333+1G>A Likely pathogenic ★★ same type
- ABCC2 c.3414+1G>A Likely pathogenic ★★ 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/abcc2-p-his1414 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown