SLC19A3 p.Gly41=
c.123A>T · rs2106332562 · VCV2651966
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.48e-05%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.18 | GERP 0.75, phastCons 0.53 |
| Overall | ||
| CADD | 7.326 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.48e-05%
European (non-Finnish) · 1/1,179,416 alleles
Overall
6.2e-05%
1/1,613,420 alleles · very rare
exomes 1/1,461,206 · genomes 0/152,214 · 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
- SLC19A3
- Protein
- p.Gly41=
- Coding
- c.123A>T
- MANE Select
- NM_025243
- dbSNP
- rs2106332562
- Type
- single nucleotide variant
- Location
- chr2:227702196 (GRCh38)
- Gene constraint
- LOEUF 0.968 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.96 · 19 PDB
Similar variants
- SLC19A3 c.1172+1G>A Pathogenic/Likely pathogenic ★★ same type
- SLC19A3 c.1172+2T>G Pathogenic ★★ same type
- SLC19A3 c.1173-1G>A Pathogenic/Likely pathogenic ★★ same type
- SLC19A3 c.151-1G>C Likely pathogenic ★★ same type
- SLC19A3 c.980-14A>G Pathogenic/Likely pathogenic ★★ same type
- SLC19A3 p.Gly23Val Pathogenic/Likely pathogenic ★★ same type
- SLC19A3 p.Met1Leu Likely pathogenic ★★ same type
- SLC19A3 p.Ser181Pro 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/slc19a3-p-gly41 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown