JPH3 p.Pro484=
c.1452C>T · VCV4931704
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0023%, eas)
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 0.065 | GERP -2.4, phastCons 0.004 |
| Overall | ||
| CADD | 4.523 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0023%
East Asian · 1/43,412 alleles
Filtering AF
0.000813%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000658%
Overall
0.00133%
21/1,581,872 alleles · very rare
exomes 20/1,429,682 · genomes 1/152,190 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0023% | 43,412 |
| Admixed American | 0.00177% | 56,596 |
| Remaining individualsnot grpmax-eligible | 0.00164% | 61,042 |
| European (non-Finnish) | 0.00137% | 72,784 |
| African / African-American | 0.00135% | 73,988 |
| South Asian | 0.00113% | 88,302 |
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
- JPH3
- Protein
- p.Pro484=
- Coding
- c.1452C>T
- MANE Select
- NM_020655
- Type
- single nucleotide variant
- Location
- chr16:87689812 (GRCh38)
- Gene constraint
- LOEUF 0.36 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 61.52
- Residue 484
- the 'disordered' region
Similar variants
- JPH3 p.Arg319Trp Uncertain significance ★★ ⚠ same type
- JPH3 p.Leu266Val Uncertain significance ★★ ⚠ same type
- JPH3 p.Thr175Met Uncertain significance ★★ ⚠ same type
- JPH3 c.2167-9C>G Benign/Likely benign ★★ same type
- JPH3 p.Ala271= Benign/Likely benign ★★ same type
- JPH3 p.Ala366= Likely benign ★★ same type
- JPH3 p.Ala384= Likely benign ★★ same type
- JPH3 p.Ala523= Benign/Likely 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/jph3-p-pro484 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown