TJP2 p.Pro987=
c.2961G>A · rs371617466 · VCV597921
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.015%, nfe)
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 -2.2 | GERP -4 |
| Overall | ||
| CADD | 8.046 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.015%
European (non-Finnish) · 177/1,177,628 alleles
Filtering AF
0.0132%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0125%
Overall
0.0113%
182/1,609,332 alleles · ultra-rare
exomes 168/1,457,144 · genomes 14/152,188 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.015% | 6,653 |
| African / African-American | 0.00535% | 18,706 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,322 |
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.Pro987=
- Coding
- c.2961G>A
- MANE Select
- NM_004817
- dbSNP
- rs371617466
- Type
- single nucleotide variant
- Location
- chr9:69249455 (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 987
- the 'disordered' region
Similar variants
- TJP2 p.Pro987Leu 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
- TJP2 p.Gln842Ter 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-pro987 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown