TYRO3 p.Pro183=
c.549C>T · rs56363203 · VCV712154
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.01%, afr)
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 -8.8 | GERP -3.4 |
| Overall | ||
| CADD | 1.783 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.01%
African / African-American · 1,510/75,030 alleles
Filtering AF
1.93%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.89%
Overall
0.103%
1,666/1,613,790 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.01% | 50 |
| Remaining individualsnot grpmax-eligible | 0.114% | 880 |
| Admixed American | 0.0967% | 1,034 |
| Middle Eastern | 0.0499% | 2,006 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00676% | 14,800 |
| East Asian | 0.00669% | 14,958 |
| South Asian | 0.0033% | 30,326 |
| Finnishnot grpmax-eligible | 0.00156% | 64,018 |
| European (non-Finnish) | 0.00127% | 78,660 |
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
- TYRO3
- Protein
- p.Pro183=
- Coding
- c.549C>T
- MANE Select
- NM_006293
- dbSNP
- rs56363203
- Type
- single nucleotide variant
- Location
- chr15:41562687 (GRCh38)
- Gene constraint
- LOEUF 0.565 · pLI 0.05 (gnomAD)
- Structure
- AlphaFold pLDDT 75.25 · 1 PDB
- Residue 183
- a disulfide bond; a β-strand; the ig-like c2-type 2 domain
Similar variants
- TYRO3 p.Ser543Phe Uncertain significance ★★ ⚠ same type
- TYRO3 p.Ala815= Benign ★★ same type
- TYRO3 p.Ala815Val Benign ★★ ⚠ same type
- TYRO3 p.Gly675Arg Benign ★★ same type
- TYRO3 p.Thr458= Benign ★★ same type
- TYRO3 p.Val669Leu Benign ★★ same type
- TYRO3 p.Ala149Ser Uncertain significance ★ ⚠ same type
- TYRO3 p.Ala149Val Uncertain significance ★ ⚠ 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/tyro3-p-pro183 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown