TNIK p.Arg511=
c.1533G>A · rs61740073 · VCV790263
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.193%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.12 | GERP -0.79, phastCons 0.46 |
| Overall | ||
| CADD | 6.149 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.193%
European (non-Finnish) · 2,273/1,179,840 alleles
Filtering AF
0.186%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.183%
Overall
0.151%
2,439/1,613,564 alleles · rare
exomes 2,318/1,461,490 · genomes 121/152,074 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.193% | 519 |
| Remaining individualsnot grpmax-eligible | 0.184% | 543 |
| Middle Eastern | 0.0494% | 2,026 |
| Admixed American | 0.035% | 2,854 |
| African / African-American | 0.0214% | 4,680 |
| Finnishnot grpmax-eligible | 0.0172% | 5,816 |
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.Arg511=
- Coding
- c.1533G>A
- MANE Select
- NM_015028
- dbSNP
- rs61740073
- Type
- single nucleotide variant
- Location
- chr3:171138266 (GRCh38)
- Gene constraint
- LOEUF 0.338 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 64.60 · 12 PDB
- Residue 511
- the 'mediates interaction with nedd4' 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-arg511 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown