ABCC6 p.Thr421=
c.1263C>T · rs114179357 · VCV384808
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 8 submitters
gnomAD v4.1
Rare
rare (popmax 0.383%, nfe)
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 -9.8 | GERP -2.3 |
| Overall | ||
| CADD | 0.147 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.383%
European (non-Finnish) · 4,517/1,179,910 alleles
Filtering AF
0.373%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.37%
Overall
0.302%
4,871/1,613,726 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.383% | 261 |
| Remaining individualsnot grpmax-eligible | 0.328% | 305 |
| Admixed American | 0.0817% | 1,224 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0811% | 1,233 |
| Middle Eastern | 0.066% | 1,514 |
| African / African-American | 0.0506% | 1,975 |
| Finnishnot grpmax-eligible | 0.0266% | 3,761 |
| South Asian | 0.0176% | 5,686 |
| East Asian | 0.00223% | 44,858 |
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
- ABCC6
- Protein
- p.Thr421=
- Coding
- c.1263C>T
- MANE Select
- NM_001171
- dbSNP
- rs114179357
- Type
- single nucleotide variant
- Location
- chr16:16198096 (GRCh38)
- Gene constraint
- LOEUF 0.917 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.32 · 4 PDB
- Residue 421
- the abc transmembrane type-1 1 domain
Similar variants
- ABCC6 p.Thr421Ala Uncertain significance ★★ ⚠ same residue
- ABCC6 p.Thr421Ile Uncertain significance ★ ⚠ same residue
- ABCC6 c.1868-5T>G Pathogenic/Likely pathogenic ★★ same type
- ABCC6 c.2071-1G>A Likely pathogenic ★★ same type
- ABCC6 c.2591-1G>T Likely pathogenic ★★ same type
- ABCC6 c.2787+1G>T Pathogenic ★★ same type
- ABCC6 c.3506+1G>A Pathogenic/Likely pathogenic ★★ same type
- ABCC6 c.3507-1G>A 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/abcc6-p-thr421 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown