SLC1A2 p.Pro144=
c.432A>G · rs768530572 · VCV2910255
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00769%, sas)
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 -3.2 | GERP -4.2 |
| Overall | ||
| CADD | 2.283 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00769%
South Asian · 7/91,086 alleles
Filtering AF
0.00359%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00255%
Overall
0.000496%
8/1,614,030 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00769% | 13,012 |
| European (non-Finnish) | 8.47e-05% | 1,180,016 |
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
- SLC1A2
- Protein
- p.Pro144=
- Coding
- c.432A>G
- MANE Select
- NM_004171
- dbSNP
- rs768530572
- Type
- single nucleotide variant
- Location
- chr11:35312327 (GRCh38)
- Gene constraint
- LOEUF 0.569 · pLI 0.84 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 77.64 · 7 PDB
- Residue 144
- a turn
Similar variants
- SLC1A2 p.Pro289Arg Pathogenic/Likely pathogenic ★★ same type
- SLC1A2 c.562-2A>G Uncertain significance ★★ same type
- SLC1A2 p.Ala210Thr Uncertain significance ★★ ⚠ same type
- SLC1A2 p.Ala293Thr Uncertain significance ★★ ⚠ same type
- SLC1A2 p.Ala349Thr Uncertain significance ★★ ⚠ same type
- SLC1A2 p.Ala349Val Uncertain significance ★★ ⚠ same type
- SLC1A2 p.Ala362Thr Uncertain significance ★★ ⚠ same type
- SLC1A2 p.Ala394Thr Uncertain significance ★★ ⚠ 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/slc1a2-p-pro144 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown