JPH2 p.Glu85=
c.255G>A · rs2515764205 · VCV2728777
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000169%, nfe)
Conditions
1
hypertrophic cardiomyopathy
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 0.56 | GERP -0.27, phastCons 1 |
| Overall | ||
| CADD | 11.37 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000169%
European (non-Finnish) · 2/1,179,994 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000124%
2/1,614,122 alleles · very rare
exomes 2/1,461,818 · genomes 0/152,304 · joint denominator
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
- JPH2
- Protein
- p.Glu85=
- Coding
- c.255G>A
- MANE Select
- NM_020433
- dbSNP
- rs2515764205
- Type
- single nucleotide variant
- Location
- chr20:44186451 (GRCh38)
- Gene constraint
- LOEUF 1.051 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 65.09 · 2 PDB
- Residue 85
- a UniProt-annotated variant site (found in a patient with dilated cardiomyopathy; likely pathogenic); a β-strand
Similar variants
- JPH2 p.Glu85Lys Uncertain significance ★★ ⚠ same residue
- JPH2 p.Thr161Lys Pathogenic/Likely pathogenic ★★ same condition
- JPH2 p.Ala181Thr Uncertain significance ★★ ⚠ same condition
- JPH2 p.Ala194Ser Uncertain significance ★★ ⚠ same condition
- JPH2 p.Ala214Glu Uncertain significance ★★ ⚠ same condition
- JPH2 p.Ala394Thr Uncertain significance ★★ ⚠ same condition
- JPH2 p.Ala401Val Uncertain significance ★★ ⚠ same condition
- JPH2 p.Ala405Thr Uncertain significance ★★ same condition
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/jph2-p-glu85 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown