SLC19A2 p.Thr196=
c.588C>T · rs146835764 · VCV761391
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0648%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.25 | acceptor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.5 | GERP -2.4, phastCons 1 |
| Overall | ||
| CADD | 13.76 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0648%
South Asian · 59/91,086 alleles
Filtering AF
0.0515%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0467%
Overall
0.0111%
179/1,614,058 alleles · ultra-rare
exomes 163/1,461,886 · genomes 16/152,172 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0648% | 1,544 |
| Middle Eastern | 0.0329% | 3,042 |
| European (non-Finnish) | 0.00958% | 10,443 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,621 |
| Admixed American | 0.00167% | 60,008 |
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
- SLC19A2
- Protein
- p.Thr196=
- Coding
- c.588C>T
- MANE Select
- NM_006996
- dbSNP
- rs146835764
- Type
- single nucleotide variant
- Location
- chr1:169477374 (GRCh38)
- Gene constraint
- LOEUF 0.852 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.99 · 2 PDB
- Residue 196
- an α-helix
Similar variants
- SLC19A2 c.1223+1G>A Pathogenic ★★ same type
- SLC19A2 c.807+2T>G Likely pathogenic ★★ same type
- SLC19A2 p.Arg162Ter Pathogenic ★★ same type
- SLC19A2 p.Arg397Ter Pathogenic/Likely pathogenic ★★ same type
- SLC19A2 p.Gln233Ter Pathogenic ★★ same type
- SLC19A2 p.Glu66Ter Pathogenic ★★ same type
- SLC19A2 p.Gly105Glu Pathogenic/Likely pathogenic ★★ same type
- SLC19A2 p.Gly172Asp 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/slc19a2-p-thr196 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown