JAM3 p.Val117=
c.351C>A · rs536759201 · VCV1957603
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 | 0.09 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.53 | GERP -2.8, phastCons 0.008 |
| Overall | ||
| CADD | 4.276 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/60,012 alleles
Overall
6.2e-05%
1/1,614,138 alleles · very rare
exomes 1/1,461,870 · genomes 0/152,268 · 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
- JAM3
- Protein
- p.Val117=
- Coding
- c.351C>A
- MANE Select
- NM_032801
- dbSNP
- rs536759201
- Type
- single nucleotide variant
- Location
- chr11:134144335 (GRCh38)
- Gene constraint
- LOEUF 1.003 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 84.67
- Residue 117
- the ig-like v-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-val117 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown