TNIK p.Ile787=
c.2361T>C · VCV4964998
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.014%, eas)
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 1 | GERP -3.6, phastCons 1 |
| Overall | ||
| CADD | 5.748 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.014%
East Asian · 6/42,884 alleles
Filtering AF
0.00601%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00409%
Overall
0.000573%
9/1,571,874 alleles · ultra-rare
exomes 6/1,419,576 · genomes 3/152,298 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.014% | 7,147 |
| Remaining individualsnot grpmax-eligible | 0.00164% | 61,008 |
| South Asian | 0.00117% | 85,246 |
| European (non-Finnish) | 8.64e-05% | 1,157,374 |
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
- TNIK
- Protein
- p.Ile787=
- Coding
- c.2361T>C
- MANE Select
- NM_015028
- Type
- single nucleotide variant
- Location
- chr3:171108086 (GRCh38)
- Gene constraint
- LOEUF 0.338 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 64.60 · 12 PDB
- Residue 787
- the 'mediates interaction with nedd4' region; the 'disordered' region
Similar variants
- TNIK p.Arg545Trp Uncertain significance ★★ ⚠ same type
- TNIK p.Arg632Cys Uncertain significance ★★ ⚠ same type
- TNIK p.Arg914Gln Uncertain significance ★★ ⚠ same type
- TNIK p.Asn1353Ser Uncertain significance ★★ ⚠ same type
- TNIK p.Gly910Glu Uncertain significance ★★ ⚠ same type
- TNIK p.Ile653Phe Uncertain significance ★★ ⚠ same type
- TNIK p.Lys913Gln Uncertain significance ★★ ⚠ same type
- TNIK c.1419+19A>G Benign ★★ 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/tnik-p-ile787 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown