SLC20A2 p.Phe623=
c.1869C>T · rs753212009 · VCV792829
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00602%, 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 -6.1 | GERP -4 |
| Overall | ||
| CADD | 0.359 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00602%
European (non-Finnish) · 71/1,179,994 alleles
Filtering AF
0.00486%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00447%
Overall
0.00458%
74/1,614,048 alleles · very rare
exomes 74/1,461,834 · genomes 0/152,214 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00602% | 16,620 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,506 |
| African / African-American | 0.00133% | 74,988 |
| South Asian | 0.0011% | 91,078 |
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.Phe623=
- Coding
- c.1869C>T
- MANE Select
- NM_001257180
- dbSNP
- rs753212009
- Type
- single nucleotide variant
- Location
- chr8:42417893 (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-phe623 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown