JPH3 p.Arg589=
c.1767G>A · rs538000829 · VCV744623
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0639%, amr)
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 1.8 | GERP -0.15, phastCons 1 |
| Overall | ||
| CADD | 7.854 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0639%
Admixed American · 37/57,938 alleles
Filtering AF
0.0475%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0419%
Overall
0.0201%
320/1,589,722 alleles · ultra-rare
exomes 269/1,437,524 · genomes 51/152,198 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0639% | 1,566 |
| Remaining individualsnot grpmax-eligible | 0.0244% | 4,095 |
| European (non-Finnish) | 0.0223% | 4,477 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00342% | 29,198 |
| South Asian | 0.00342% | 29,213 |
| African / African-American | 0.0027% | 37,062 |
| East Asian | 0.00232% | 43,092 |
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.Arg589=
- Coding
- c.1767G>A
- MANE Select
- NM_020655
- dbSNP
- rs538000829
- Type
- single nucleotide variant
- Location
- chr16:87690127 (GRCh38)
- Gene constraint
- LOEUF 0.36 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 61.52
- Residue 589
- the 'disordered' region
Similar variants
- JPH3 p.Arg589Gln Uncertain significance ★ ⚠ same residue
- 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
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-arg589 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown