LATS2 p.Pro519=
c.1557G>A · rs139641767 · VCV711578
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.755%, 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 -3.7 | GERP -3.7 |
| Overall | ||
| CADD | 4.239 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.755%
African / African-American · 566/74,946 alleles
Filtering AF
0.704%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.683%
Overall
0.0482%
775/1,608,160 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.755% | 132 |
| Remaining individualsnot grpmax-eligible | 0.107% | 931 |
| Admixed American | 0.087% | 1,150 |
| Middle Eastern | 0.0496% | 2,017 |
| East Asian | 0.0223% | 4,485 |
| European (non-Finnish) | 0.00644% | 15,517 |
| South Asian | 0.0011% | 90,940 |
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
- LATS2
- Protein
- p.Pro519=
- Coding
- c.1557G>A
- MANE Select
- NM_014572
- dbSNP
- rs139641767
- Type
- single nucleotide variant
- Location
- chr13:20988223 (GRCh38)
- Gene constraint
- LOEUF 0.493 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 56.73 · 1 PDB
Similar variants
- LATS2 p.Pro519Ser Uncertain significance ★ ⚠ same residue
- LATS2 c.2665+5A>G Benign ★★ same type
- LATS2 p.Arg378= Benign/Likely benign ★★ same type
- LATS2 p.Asp1013Asn Benign ★★ same type
- LATS2 p.Asp534= Benign ★★ same type
- LATS2 p.Asp852Glu Benign ★★ same type
- LATS2 p.Gly563Arg Benign ★★ same type
- LATS2 p.Leu386= Benign ★★ 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/lats2-p-pro519 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown