LATS2 p.Pro280=
c.840G>T · rs201011483 · VCV711579
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.21%, afr)
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 -6.1 | GERP -3.1 |
| Overall | ||
| CADD | 0.129 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.21%
African / African-American · 2,338/72,918 alleles
Filtering AF
3.1%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.05%
Overall
0.172%
2,626/1,527,816 alleles · low-frequency
exomes 1,256/1,375,564 · genomes 1,370/152,252 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.21% | 31 |
| Middle Eastern | 0.243% | 411 |
| Remaining individualsnot grpmax-eligible | 0.202% | 494 |
| Admixed American | 0.167% | 600 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0538% | 1,860 |
| South Asian | 0.006% | 16,676 |
| European (non-Finnish) | 0.00456% | 21,947 |
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.Pro280=
- Coding
- c.840G>T
- MANE Select
- NM_014572
- dbSNP
- rs201011483
- Type
- single nucleotide variant
- Location
- chr13:20988940 (GRCh38)
- Gene constraint
- LOEUF 0.493 · pLI 0.98 (gnomAD)
- Structure
- AlphaFold pLDDT 56.73 · 1 PDB
- Residue 280
- the 'disordered' region
Similar variants
- 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
- LATS2 p.Pro519= 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-pro280 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown