SLC40A1 p.Val511=
c.1533C>T · rs1574236070 · VCV764711
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.47e-05%, nfe)
Conditions
1
hemochromatosis type 4
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 -1.2, phastCons 1 |
| Overall | ||
| CADD | 5.666 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.47e-05%
European (non-Finnish) · 1/1,179,982 alleles
Overall
6.84e-05%
1/1,461,740 alleles · very rare
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
- SLC40A1
- Protein
- p.Val511=
- Coding
- c.1533C>T
- MANE Select
- NM_014585
- dbSNP
- rs1574236070
- Type
- single nucleotide variant
- Location
- chr2:189562061 (GRCh38)
- Gene constraint
- LOEUF 0.445 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 80.26 · 8 PDB
- Residue 511
- an α-helix
Similar variants
- SLC40A1 p.Val511Ile Conflicting classifications of pathogenicity ★ ⚠ same residue
- SLC40A1 p.Arg178Gln Pathogenic/Likely pathogenic ★★ same condition
- SLC40A1 p.Arg88Gly Pathogenic/Likely pathogenic ★★ same condition
- SLC40A1 p.Arg88Thr Pathogenic/Likely pathogenic ★★ same condition
- SLC40A1 p.Asn144Asp Pathogenic ★★ ⚠ same condition
- SLC40A1 p.Asp157Gly Likely pathogenic ★★ same condition
- SLC40A1 p.Cys326Tyr Pathogenic ★★ ⚠ same condition
- SLC40A1 p.Gly204Ser 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/slc40a1-p-val511 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown