JAM2 p.Val244=
c.732A>G · VCV4453401
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.26%, sas)
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 -2.7 | GERP -3.8 |
| Overall | ||
| CADD | 0.672 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.26%
South Asian · 1,152/91,082 alleles
Filtering AF
1.2%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.18%
Overall
0.0763%
1,231/1,613,796 alleles · low-frequency
exomes 1,145/1,461,452 · genomes 86/152,344 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 1.26% | 79 |
| Remaining individualsnot grpmax-eligible | 0.0848% | 1,179 |
| Middle Eastern | 0.066% | 1,516 |
| Admixed American | 0.00666% | 15,006 |
| African / African-American | 0.004% | 25,017 |
| European (non-Finnish) | 0.00127% | 78,644 |
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
- JAM2
- Protein
- p.Val244=
- Coding
- c.732A>G
- MANE Select
- NM_021219
- Type
- single nucleotide variant
- Location
- chr21:25706013 (GRCh38)
- Gene constraint
- LOEUF 0.93 · pLI 0.09 (gnomAD)
- Structure
- AlphaFold pLDDT 82.91
- Residue 244
- a UniProt-annotated variant site (in ibgc8); a UniProt-annotated variant site (in ibgc8; loss of protein expression)
Similar variants
- JAM2 p.Val244Ala Uncertain significance ★ ⚠ same residue
- JAM2 p.Val244Ile Uncertain significance ★ ⚠ same residue
- JAM2 p.Arg229Ter Pathogenic ★★ same type
- JAM2 c.68-96C>A Benign ★★ same type
- JAM2 c.697+127C>T Benign ★★ same type
- JAM2 c.698-21G>A Benign ★★ same type
- JAM2 c.805+30T>A Benign ★★ same type
- JAM2 c.806-21T>G 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/jam2-p-val244 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown