SLC20A2 p.Phe229=
c.687T>C · rs144390898 · VCV734005
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.135%, 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 -1.5 | GERP -3.7 |
| Overall | ||
| CADD | 0.834 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.135%
African / African-American · 101/75,028 alleles
Filtering AF
0.113%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.105%
Overall
0.00713%
115/1,613,044 alleles · rare
exomes 54/1,460,748 · genomes 61/152,296 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.135% | 743 |
| Remaining individualsnot grpmax-eligible | 0.00961% | 10,408 |
| Admixed American | 0.00667% | 14,993 |
| European (non-Finnish) | 0.000339% | 294,798 |
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
- SLC20A2
- Protein
- p.Phe229=
- Coding
- c.687T>C
- MANE Select
- NM_001257180
- dbSNP
- rs144390898
- Type
- single nucleotide variant
- Location
- chr8:42444689 (GRCh38)
- Gene constraint
- LOEUF 0.644 · pLI 0.02 (gnomAD)
- Structure
- AlphaFold pLDDT 72.63
Similar variants
- SLC20A2 c.1794+1G>C Pathogenic/Likely pathogenic ★★ same type
- SLC20A2 c.290-8A>G Pathogenic ★★ same type
- SLC20A2 c.935-2A>G Pathogenic ★★ same type
- SLC20A2 p.Arg382Ter Pathogenic ★★ same type
- SLC20A2 p.Arg467Ter Pathogenic ★★ same type
- SLC20A2 p.Asp28Asn Pathogenic/Likely pathogenic ★★ same type
- SLC20A2 p.Gln46Ter Pathogenic ★★ same type
- SLC20A2 p.Glu459Ter 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/slc20a2-p-phe229 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown