SLC15A2 p.Ser445=
c.1335C>T · rs144786366 · VCV717874
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.89%, eas)
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 -1.8 | GERP -0.79 |
| Overall | ||
| CADD | 8.438 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.89%
East Asian · 1,297/44,876 alleles
Filtering AF
2.76%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.71%
Overall
0.119%
1,918/1,613,952 alleles · low-frequency
exomes 1,661/1,461,650 · genomes 257/152,302 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 2.89% | 35 |
| Ashkenazi Jewishnot grpmax-eligible | 0.922% | 108 |
| Remaining individualsnot grpmax-eligible | 0.302% | 331 |
| Middle Eastern | 0.066% | 1,514 |
| Admixed American | 0.06% | 1,667 |
| South Asian | 0.0516% | 1,937 |
| African / African-American | 0.02% | 5,002 |
| European (non-Finnish) | 0.00483% | 20,700 |
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
- SLC15A2
- Protein
- p.Ser445=
- Coding
- c.1335C>T
- MANE Select
- NM_021082
- dbSNP
- rs144786366
- Type
- single nucleotide variant
- Location
- chr3:121928549 (GRCh38)
- Gene constraint
- LOEUF 1.153 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.17 · 4 PDB
- Residue 445
- the 'extracellular domain (ecd)' region
Similar variants
- SLC15A2 p.Ala47Gly Uncertain significance ★ ⚠ same type
- SLC15A2 p.Arg25Pro Uncertain significance ★ ⚠ same type
- SLC15A2 p.Arg277Gln Uncertain significance ★ ⚠ same type
- SLC15A2 p.Arg322Gln Uncertain significance ★ ⚠ same type
- SLC15A2 p.Arg329Ser Uncertain significance ★ ⚠ same type
- SLC15A2 p.Asn538Asp Uncertain significance ★ ⚠ same type
- SLC15A2 p.Asn604Lys Uncertain significance ★ ⚠ same type
- SLC15A2 p.Asp360Asn 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/slc15a2-p-ser445 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown