LAT p.Pro85=
c.255G>A · rs200258693 · VCV1592590
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.118%, eas)
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 -5.5 | |
| Overall | ||
| CADD | 0.623 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.118%
East Asian · 53/44,862 alleles
Filtering AF
0.0927%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0836%
Overall
0.007%
113/1,613,590 alleles · rare
exomes 105/1,461,428 · genomes 8/152,162 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.118% | 846 |
| Admixed American | 0.0117% | 8,569 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,833 |
| European (non-Finnish) | 0.00398% | 25,107 |
| Finnishnot grpmax-eligible | 0.00315% | 31,788 |
| South Asian | 0.0011% | 91,078 |
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
- LAT
- Protein
- p.Pro85=
- Coding
- c.255G>A
- MANE Select
- NM_001014987
- dbSNP
- rs200258693
- Type
- single nucleotide variant
- Location
- chr16:28986391 (GRCh38)
- Gene constraint
- LOEUF 0.474 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 59.77
- Residue 85
- the 'disordered' region
Similar variants
- LAT c.-41G>T Uncertain significance ★★ same type
- LAT p.Ala183Val Uncertain significance ★★ ⚠ same type
- LAT p.Arg53Gln Uncertain significance ★★ ⚠ same type
- LAT p.Arg93Gln Uncertain significance ★★ ⚠ same type
- LAT p.Arg93Trp Uncertain significance ★★ ⚠ same type
- LAT p.Arg98Gln Uncertain significance ★★ ⚠ same type
- LAT p.Arg98Trp Uncertain significance ★★ ⚠ same type
- LAT p.Asp126Val 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/lat-p-pro85 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown