PLP2 p.Pro147=
c.441C>T · rs141287647 · VCV2660512
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0386%, 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 -0.64 | GERP -3.4, phastCons 0.078 |
| Overall | ||
| CADD | 4.153 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0386%
African / African-American · 22/57,012 alleles
Filtering AF
0.0261%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0221%
Overall
0.00307%
37/1,204,970 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0386% | 2,591 |
| Remaining individualsnot grpmax-eligible | 0.0126% | 7,908 |
| East Asian | 0.0118% | 8,440 |
| Admixed American | 0.00219% | 45,674 |
| European (non-Finnish) | 0.000449% | 222,724 |
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
- PLP2
- Protein
- p.Pro147=
- Coding
- c.441C>T
- MANE Select
- NM_002668
- dbSNP
- rs141287647
- Type
- single nucleotide variant
- Location
- chrX:49174676 (GRCh38)
- Structure
- AlphaFold pLDDT 78.76
Similar variants
- PLP2 p.Arg6Cys Benign ★★ same type
- PLP2 p.Ala121Pro Uncertain significance ★ ⚠ same type
- PLP2 p.Ala2Val Uncertain significance ★ ⚠ same type
- PLP2 p.Arg136Trp Uncertain significance ★ ⚠ same type
- PLP2 p.Arg21His Uncertain significance ★ ⚠ same type
- PLP2 p.Arg87Gln Uncertain significance ★ ⚠ same type
- PLP2 p.Gly118Ser Uncertain significance ★ ⚠ same type
- PLP2 p.Ile33Val 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/plp2-p-pro147 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown