TJP2 p.Pro897=
c.2691C>T · rs149969431 · VCV178679
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 7 submitters
gnomAD v4.1
Rare
rare (popmax 0.575%, afr)
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 -7.1 | GERP -4 |
| Overall | ||
| CADD | 4.816 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.575%
African / African-American · 431/74,976 alleles
Filtering AF
0.53%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.512%
Overall
0.031%
499/1,610,234 alleles · rare
exomes 246/1,457,954 · genomes 253/152,280 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.575% | 174 |
| Remaining individualsnot grpmax-eligible | 0.0417% | 2,398 |
| Middle Eastern | 0.0331% | 3,021 |
| Admixed American | 0.0267% | 3,742 |
| South Asian | 0.00772% | 12,956 |
| European (non-Finnish) | 0.00144% | 69,254 |
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.Pro897=
- Coding
- c.2691C>T
- MANE Select
- NM_004817
- dbSNP
- rs149969431
- Type
- single nucleotide variant
- Location
- chr9:69248035 (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 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
- TJP2 p.Gln842Ter Pathogenic ★★ same type
- TJP2 p.Gln878Ter 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-pro897 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown