JAM3 p.Ser307=
c.921G>A · rs144672452 · VCV789802
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.673%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.134 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP -5.1 | GERP -3.8 |
| Overall | ||
| CADD | 2.337 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.673%
African / African-American · 505/75,054 alleles
Filtering AF
0.624%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.605%
Overall
0.0345%
557/1,613,986 alleles · rare
exomes 284/1,461,666 · genomes 273/152,320 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.673% | 149 |
| Remaining individualsnot grpmax-eligible | 0.0368% | 2,717 |
| Admixed American | 0.025% | 4,001 |
| South Asian | 0.00329% | 30,359 |
| East Asian | 0.00223% | 44,886 |
| European (non-Finnish) | 0.000848% | 117,987 |
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.Ser307=
- Coding
- c.921G>A
- MANE Select
- NM_032801
- dbSNP
- rs144672452
- Type
- single nucleotide variant
- Location
- chr11:134149169 (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 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
- JAM3 p.Arg185Ile Uncertain significance ★★ ⚠ same type
- JAM3 p.Arg191Cys 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-ser307 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown