SLC45A2 p.Arg348=
c.1044C>T · rs533984191 · VCV773698
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0401%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.102 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -9.6 | GERP -5.5 |
| Overall | ||
| CADD | 0.064 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0401%
East Asian · 18/44,882 alleles
Filtering AF
0.0259%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0214%
Overall
0.00273%
44/1,614,126 alleles · ultra-rare
exomes 38/1,461,872 · genomes 6/152,254 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0401% | 2,493 |
| African / African-American | 0.00666% | 15,006 |
| South Asian | 0.00549% | 18,214 |
| Admixed American | 0.005% | 20,005 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,837 |
| European (non-Finnish) | 0.000847% | 118,001 |
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.Arg348=
- Coding
- c.1044C>T
- MANE Select
- NM_016180
- dbSNP
- rs533984191
- Type
- single nucleotide variant
- Location
- chr5:33951666 (GRCh38)
- Gene constraint
- LOEUF 1.022 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 77.96
- Residue 348
- a UniProt-annotated variant site (in oca4)
Similar variants
- SLC45A2 p.Arg348Cys Uncertain significance ★★ ⚠ same residue
- SLC45A2 p.Arg348Pro Uncertain significance ★★ same residue
- SLC45A2 p.Arg348His 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
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-arg348 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown