LAT p.Pro175=
c.525G>A · rs764430069 · VCV1443220
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0201%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.21 | acceptor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -11 | |
| Overall | ||
| CADD | 6.435 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0201%
Admixed American · 12/59,672 alleles
Filtering AF
0.0116%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00903%
Overall
0.00608%
98/1,611,368 alleles · ultra-rare
exomes 78/1,459,232 · genomes 20/152,136 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0201% | 4,973 |
| Remaining individualsnot grpmax-eligible | 0.00962% | 10,397 |
| European (non-Finnish) | 0.00662% | 15,110 |
| African / African-American | 0.00267% | 37,440 |
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.Pro175=
- Coding
- c.525G>A
- MANE Select
- NM_001014987
- dbSNP
- rs764430069
- Type
- single nucleotide variant
- Location
- chr16:28989558 (GRCh38)
- Gene constraint
- LOEUF 0.474 · pLI 0.99 (gnomAD)
- Structure
- AlphaFold pLDDT 59.77
Similar variants
- LAT p.Pro175Leu 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-pro175 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown