SLC45A1 p.Pro3=
c.9C>T · rs138622022 · VCV3051263
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.117%, afr)
Conditions
1
SLC45A1-related disorder
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 0.06 | GERP -2.3, phastCons 0.002 |
| Overall | ||
| CADD | 10.02 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.117%
African / African-American · 88/75,006 alleles
Filtering AF
0.0975%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0902%
Overall
0.0112%
181/1,612,260 alleles · rare
exomes 127/1,460,046 · genomes 54/152,214 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.117% | 852 |
| Middle Eastern | 0.0991% | 1,009 |
| South Asian | 0.0209% | 4,791 |
| Remaining individualsnot grpmax-eligible | 0.016% | 6,248 |
| Admixed American | 0.005% | 20,001 |
| European (non-Finnish) | 0.00458% | 21,846 |
| East Asian | 0.00223% | 44,846 |
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
- SLC45A1
- Protein
- p.Pro3=
- Coding
- c.9C>T
- MANE Select
- NM_001080397
- dbSNP
- rs138622022
- Type
- single nucleotide variant
- Location
- chr1:8324338 (GRCh38)
- Gene constraint
- LOEUF 0.695 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 66.26
Disease context
SLC45A1-related disorder
Similar variants
- SLC45A1 p.Pro340Leu Uncertain significance ★★ same condition
- SLC45A1 p.Val18Met Uncertain significance ★ ⚠ same condition
- SLC45A1 c.1774+6C>T Likely benign same condition
- SLC45A1 p.Ala302= Likely benign same condition
- SLC45A1 p.Pro312= Likely benign same condition
- SLC45A1 p.Pro62= Likely benign same condition
- SLC45A1 p.Ser59= Likely benign same condition
- SLC45A1 p.Val247= Likely benign same condition
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/slc45a1-p-pro3 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown