SLC45A2 p.Phe189=
c.567T>C · rs2478841644 · VCV1996847
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
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 0.48 | GERP -3.1, phastCons 0.85 |
| Overall | ||
| CADD | 6.063 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- SLC45A2
- Protein
- p.Phe189=
- Coding
- c.567T>C
- MANE Select
- NM_016180
- dbSNP
- rs2478841644
- Type
- single nucleotide variant
- Location
- chr5:33964012 (GRCh38)
- Gene constraint
- LOEUF 1.022 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.96
Similar variants
- SLC45A2 c.1156+1G>C Pathogenic/Likely pathogenic ★★ same type
- SLC45A2 c.386-1G>A Pathogenic ★★ same type
- SLC45A2 p.Ala486Thr Pathogenic/Likely pathogenic ★★ same type
- SLC45A2 p.Ala511Glu Pathogenic ★★ same type
- SLC45A2 p.Arg102Gln Pathogenic/Likely pathogenic ★★ same type
- SLC45A2 p.Asn122Ser Pathogenic/Likely pathogenic ★★ ⚠ same type
- SLC45A2 p.Asp157Asn Pathogenic ★★ ⚠ same type
- SLC45A2 p.Asp160His Pathogenic/Likely 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/slc45a2-p-phe189 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown