LAT p.Asp42=
c.126T>C · rs139864999 · VCV2059212
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.165%, afr)
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 -2 | |
| Overall | ||
| CADD | 0.909 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.165%
African / African-American · 124/75,018 alleles
Filtering AF
0.142%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.133%
Overall
0.00861%
139/1,614,020 alleles · rare
exomes 71/1,461,810 · genomes 68/152,210 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.165% | 605 |
| Remaining individualsnot grpmax-eligible | 0.0192% | 5,209 |
| Admixed American | 0.00167% | 60,012 |
| European (non-Finnish) | 0.000169% | 589,995 |
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.Asp42=
- Coding
- c.126T>C
- MANE Select
- NM_001014987
- dbSNP
- rs139864999
- Type
- single nucleotide variant
- Location
- chr16:28985738 (GRCh38)
- Gene constraint
- LOEUF 0.474 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 59.77
Similar variants
- LAT p.Asp42fs Pathogenic ★ 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-asp42 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown