SLC45A2 p.Ser3=
c.9C>T · rs2112022379 · VCV1671705
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,609,682)
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 3.6 | GERP -1.2, phastCons 0.69 |
| Overall | ||
| CADD | 8.898 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,609,682). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- SLC45A2
- Protein
- p.Ser3=
- Coding
- c.9C>T
- MANE Select
- NM_016180
- dbSNP
- rs2112022379
- Type
- single nucleotide variant
- Location
- chr5:33984575 (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-ser3 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown