JAM3 p.Arg295=
c.885C>T · VCV4700266
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00167%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.201 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP 3.5 | GERP -0.18, phastCons 1 |
| Overall | ||
| CADD | 7.455 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/60,028 alleles
Filtering AF
0.000247%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000159%
Overall
0.000496%
8/1,614,040 alleles · very rare
exomes 8/1,461,764 · genomes 0/152,276 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00167% | 60,028 |
| European (non-Finnish) | 0.000593% | 168,559 |
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
- JAM3
- Protein
- p.Arg295=
- Coding
- c.885C>T
- MANE Select
- NM_032801
- Type
- single nucleotide variant
- Location
- chr11:134148806 (GRCh38)
- Gene constraint
- LOEUF 1.003 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 84.67
Similar variants
- JAM3 p.Arg295His Uncertain significance ★ ⚠ same residue
- JAM3 p.Arg295Cys Likely benign ★ same residue
- JAM3 c.612+1G>T Pathogenic ★★ same type
- JAM3 p.Ala2Ser Uncertain significance ★★ ⚠ same type
- JAM3 p.Arg107Trp Uncertain significance ★★ same type
- JAM3 p.Arg123Cys Uncertain significance ★★ ⚠ same type
- JAM3 p.Arg14Trp Uncertain significance ★★ ⚠ same type
- JAM3 p.Arg168Gln Uncertain significance ★★ ⚠ 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/jam3-p-arg295 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown