TJP2 p.Ala882=
c.2646G>A · rs11788754 · VCV44098
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 7 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.51%, mid)
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 -0.29 | GERP -4.3, phastCons 0.001 |
| Overall | ||
| CADD | 7.144 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.51%
Middle Eastern · 152/6,062 alleles
Filtering AF
2.18%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.06%
Overall
1.75%
28,266/1,614,012 alleles · low-frequency
exomes 26,248/1,461,758 · genomes 2,018/152,254 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 2.51% | 40 |
| European (non-Finnish) | 2.04% | 49 |
| South Asian | 1.91% | 52 |
| Remaining individualsnot grpmax-eligible | 1.47% | 68 |
| Ashkenazi Jewishnot grpmax-eligible | 1.38% | 72 |
| Admixed American | 0.913% | 110 |
| Amishnot grpmax-eligible | 0.879% | 114 |
| African / African-American | 0.356% | 281 |
| Finnishnot grpmax-eligible | 0.305% | 328 |
| East Asian | 0.00446% | 22,434 |
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
- TJP2
- Protein
- p.Ala882=
- Coding
- c.2646G>A
- MANE Select
- NM_004817
- dbSNP
- rs11788754
- Type
- single nucleotide variant
- Location
- chr9:69246769 (GRCh38)
- Gene constraint
- LOEUF 0.825 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 62.92 · 2 PDB
Similar variants
- TJP2 p.Ala882Glu Uncertain significance ★ ⚠ same residue
- TJP2 p.Ala882Val Uncertain significance ★ ⚠ same residue
- TJP2 c.239+1G>A Pathogenic/Likely pathogenic ★★ same type
- TJP2 p.Arg412Ter Pathogenic ★★ same type
- TJP2 p.Arg591Ter Pathogenic ★★ same type
- TJP2 p.Arg632Ter Pathogenic ★★ same type
- TJP2 p.Arg725Ter Pathogenic ★★ same type
- TJP2 p.Gln207Ter Pathogenic/Likely pathogenic ★★ 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/tjp2-p-ala882 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown