TJP2 p.Pro71=
c.213G>A · rs780781603 · VCV1310914
Uncertain significance
Multiple submitters
Classification
Uncertain significance
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00446%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.83 | donor gain · deltas |
|---|---|---|
| Pangolin | Δ0.43 | gain · loss 0.12 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP -11 | GERP -4.3 |
| Overall | ||
| CADD | 16.45 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00446%
East Asian · 2/44,892 alleles
Filtering AF
0.000738%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000276%
Overall
0.000434%
7/1,614,122 alleles · very rare
exomes 7/1,461,864 · genomes 0/152,258 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00446% | 22,446 |
| Admixed American | 0.00333% | 30,007 |
| European (non-Finnish) | 0.000254% | 393,338 |
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.Pro71=
- Coding
- c.213G>A
- MANE Select
- NM_004817
- dbSNP
- rs780781603
- Type
- single nucleotide variant
- Location
- chr9:69216437 (GRCh38)
- Gene constraint
- LOEUF 0.825 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 62.92 · 2 PDB
- Residue 71
- the pdz 1 domain
Similar variants
- TJP2 p.Pro71Gln Uncertain significance ★ ⚠ same residue
- TJP2 p.Pro71Leu Conflicting classifications of pathogenicity ★ ⚠ 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-pro71 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown