JPH2 p.Asp504=
c.1512C>T · rs2145838656 · VCV1629365
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 9.13e-05%, 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 0.099 | GERP 0.76, phastCons 0.63 |
| Overall | ||
| CADD | 4.088 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
9.13e-05%
European (non-Finnish) · 1/1,095,228 alleles
Overall
7.07e-05%
1/1,415,420 alleles · very rare
exomes 1/1,263,310 · genomes 0/152,110 · 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.Asp504=
- Coding
- c.1512C>T
- MANE Select
- NM_020433
- dbSNP
- rs2145838656
- Type
- single nucleotide variant
- Location
- chr20:44116163 (GRCh38)
- Gene constraint
- LOEUF 1.051 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 65.09 · 2 PDB
- Residue 504
- the 'disordered' region; a UniProt-annotated variant site (in cmd2e; uncertain significance)
Similar variants
- 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
- JPH2 p.Ala419Ser 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-asp504 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown