JAM3 p.Pro147=
c.441G>A · rs371009569 · VCV715029
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0134%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.008 | strongly benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
| Constraint at this position | ||
| Conservation | phyloP -9.7 | GERP -2.5 |
| Overall | ||
| CADD | 0.058 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0134%
African / African-American · 10/74,886 alleles
Filtering AF
0.00723%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0055%
Overall
0.00136%
22/1,613,964 alleles · ultra-rare
exomes 16/1,461,878 · genomes 6/152,086 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0134% | 7,489 |
| East Asian | 0.00668% | 14,960 |
| South Asian | 0.0022% | 45,539 |
| Admixed American | 0.00167% | 60,002 |
| European (non-Finnish) | 0.000508% | 196,670 |
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.Pro147=
- Coding
- c.441G>A
- MANE Select
- NM_032801
- dbSNP
- rs371009569
- Type
- single nucleotide variant
- Location
- chr11:134144823 (GRCh38)
- Gene constraint
- LOEUF 1.003 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 84.67
- Residue 147
- the ig-like c2-type domain
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-pro147 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown