PHLPP2 p.Leu327=
c.981C>T · rs145216542 · VCV2646802
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.88%, mid)
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 | GERP 2.1, phastCons 1 |
| Overall | ||
| CADD | 6.615 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.88%
Middle Eastern · 114/6,062 alleles
Filtering AF
1.6%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.5%
Overall
0.103%
1,667/1,613,822 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 1.88% | 53 |
| Ashkenazi Jewishnot grpmax-eligible | 1.69% | 59 |
| Remaining individualsnot grpmax-eligible | 0.24% | 417 |
| Admixed American | 0.19% | 526 |
| European (non-Finnish) | 0.0634% | 1,577 |
| South Asian | 0.0296% | 3,373 |
| African / African-American | 0.0173% | 5,772 |
| Finnishnot grpmax-eligible | 0.00156% | 64,024 |
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
- PHLPP2
- Protein
- p.Leu327=
- Coding
- c.981C>T
- MANE Select
- NM_015020
- dbSNP
- rs145216542
- Type
- single nucleotide variant
- Location
- chr16:71679445 (GRCh38)
- Gene constraint
- LOEUF 0.684 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.11
Similar variants
- PHLPP2 p.Asp453Gly Uncertain significance ★★ ⚠ same type
- PHLPP2 p.Ile204Val Likely benign ★★ same type
- PHLPP2 p.Ser1139Cys Likely benign ★★ same type
- PHLPP2 p.Ala1008Thr Uncertain significance ★ ⚠ same type
- PHLPP2 p.Ala1008Val Uncertain significance ★ ⚠ same type
- PHLPP2 p.Ala1270Ser Uncertain significance ★ ⚠ same type
- PHLPP2 p.Ala1322Val Uncertain significance ★ ⚠ same type
- PHLPP2 p.Ala223Pro 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/phlpp2-p-leu327 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown