LAT p.Arg83=
c.249A>G · rs761916378 · VCV1929867
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00102%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.30 | acceptor loss, 30 bp away · masked 0 · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.52 | phastCons 0.93 |
| Overall | ||
| CADD | 8.565 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00102%
European (non-Finnish) · 12/1,179,986 alleles
Filtering AF
0.000542%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000428%
Overall
0.000744%
12/1,613,510 alleles · very rare
exomes 12/1,461,414 · genomes 0/152,096 · 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
- LAT
- Protein
- p.Arg83=
- Coding
- c.249A>G
- MANE Select
- NM_001014987
- dbSNP
- rs761916378
- Type
- single nucleotide variant
- Location
- chr16:28986385 (GRCh38)
- Gene constraint
- LOEUF 0.474 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 59.77
- Residue 83
- the 'disordered' region
Similar variants
- LAT p.Arg83Gly Uncertain significance ★ same residue
- 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
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-arg83 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown