SLC11A2 p.Phe47=
c.141C>T · VCV3711334
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0156%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.27 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.23 | GERP -3.3 |
| Overall | ||
| CADD | 6.906 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0156%
East Asian · 7/44,860 alleles
Filtering AF
0.00773%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00579%
Overall
0.00316%
51/1,613,152 alleles · ultra-rare
exomes 41/1,461,060 · genomes 10/152,092 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0156% | 6,409 |
| Admixed American | 0.015% | 6,665 |
| South Asian | 0.0121% | 8,277 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,825 |
| European (non-Finnish) | 0.0017% | 58,964 |
| African / African-American | 0.00133% | 74,946 |
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
- SLC11A2
- Protein
- p.Phe47=
- Coding
- c.141C>T
- MANE Select
- NM_000617
- Type
- single nucleotide variant
- Location
- chr12:51008518 (GRCh38)
- Gene constraint
- LOEUF 0.78 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.83 · 7 PDB
Similar variants
- SLC11A2 p.Ala555Thr Uncertain significance ★★ same type
- SLC11A2 p.Arg557His Uncertain significance ★★ same type
- SLC11A2 p.Asn311Ser Uncertain significance ★★ ⚠ same type
- SLC11A2 p.Glu320Lys Uncertain significance ★★ ⚠ same type
- SLC11A2 p.Ser350Leu Uncertain significance ★★ ⚠ same type
- SLC11A2 p.Ser66Asn Uncertain significance ★★ ⚠ same type
- SLC11A2 p.Thr543Lys Uncertain significance ★★ ⚠ same type
- SLC11A2 p.Val186Ile Uncertain significance ★★ ⚠ 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/slc11a2-p-phe47 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown