TJP2 p.Ser953=
c.2859G>T · rs369972534 · VCV165420
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
rare (popmax 0.446%, 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 -5.2 | GERP -4.3 |
| Overall | ||
| CADD | 0.154 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.446%
Middle Eastern · 27/6,052 alleles
Filtering AF
0.315%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.271%
Overall
0.0184%
295/1,606,538 alleles · rare
exomes 277/1,454,252 · genomes 18/152,286 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.446% | 224 |
| Remaining individualsnot grpmax-eligible | 0.0241% | 4,147 |
| South Asian | 0.021% | 4,753 |
| European (non-Finnish) | 0.0195% | 5,136 |
| Admixed American | 0.00513% | 19,500 |
| Finnishnot grpmax-eligible | 0.00157% | 63,568 |
| African / African-American | 0.00134% | 74,880 |
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.Ser953=
- Coding
- c.2859G>T
- MANE Select
- NM_004817
- dbSNP
- rs369972534
- Type
- single nucleotide variant
- Location
- chr9:69248203 (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 953
- the 'disordered' region
Similar variants
- TJP2 p.Ser953Leu 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-ser953 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown