JPH3 p.Ser169=
c.507C>T · rs35224773 · VCV733127
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.281%, nfe)
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 -1.7 | GERP -3 |
| Overall | ||
| CADD | 8.899 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.281%
European (non-Finnish) · 3,315/1,179,884 alleles
Filtering AF
0.273%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.27%
Overall
0.226%
3,653/1,612,880 alleles · rare
exomes 3,417/1,460,502 · genomes 236/152,378 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.281% | 356 |
| Remaining individualsnot grpmax-eligible | 0.264% | 379 |
| Admixed American | 0.107% | 938 |
| Finnishnot grpmax-eligible | 0.0556% | 1,798 |
| African / African-American | 0.048% | 2,085 |
| South Asian | 0.0285% | 3,503 |
| East Asian | 0.0223% | 4,487 |
| Middle Eastern | 0.0165% | 6,062 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,578 |
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.Ser169=
- Coding
- c.507C>T
- MANE Select
- NM_020655
- dbSNP
- rs35224773
- Type
- single nucleotide variant
- Location
- chr16:87644382 (GRCh38)
- Gene constraint
- LOEUF 0.36 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 61.52
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-ser169 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown