SLC45A2 p.Pro86=
c.258C>T · rs749383458 · VCV2815041
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00144%, 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 -8 | GERP -4.3 |
| Overall | ||
| CADD | 0.443 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00144%
European (non-Finnish) · 17/1,180,012 alleles
Filtering AF
0.000878%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000717%
Overall
0.00105%
17/1,613,954 alleles · very rare
exomes 16/1,461,754 · genomes 1/152,200 · joint denominator
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
- SLC45A2
- Protein
- p.Pro86=
- Coding
- c.258C>T
- MANE Select
- NM_016180
- dbSNP
- rs749383458
- Type
- single nucleotide variant
- Location
- chr5:33984326 (GRCh38)
- Gene constraint
- LOEUF 1.022 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.96
Similar variants
- SLC45A2 p.Pro86Ser Uncertain significance ★ ⚠ same residue
- 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
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-pro86 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown