LAT p.Cys9=
c.27C>T · rs780099847 · VCV2910748
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.02%, amr)
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 -7 | |
| Overall | ||
| CADD | 0.962 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.02%
Admixed American · 12/60,002 alleles
Filtering AF
0.0115%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00898%
Overall
0.00285%
46/1,613,636 alleles · ultra-rare
exomes 36/1,461,482 · genomes 10/152,154 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.02% | 5,000 |
| East Asian | 0.00668% | 14,961 |
| Finnishnot grpmax-eligible | 0.0047% | 21,270 |
| South Asian | 0.00329% | 30,363 |
| African / African-American | 0.00267% | 37,458 |
| European (non-Finnish) | 0.00186% | 53,633 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,466 |
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.Cys9=
- Coding
- c.27C>T
- MANE Select
- NM_001014987
- dbSNP
- rs780099847
- Type
- single nucleotide variant
- Location
- chr16:28985444 (GRCh38)
- Gene constraint
- LOEUF 0.474 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 59.77
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-cys9 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown