TYROBP p.Ser89=
c.267G>A · rs760509495 · VCV1547938
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0588%, 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 -8.1 | GERP -3.7 |
| Overall | ||
| CADD | 2.172 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0588%
African / African-American · 44/74,836 alleles
Filtering AF
0.0449%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0401%
Overall
0.00655%
105/1,603,400 alleles · ultra-rare
exomes 75/1,451,302 · genomes 30/152,098 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0588% | 1,701 |
| Remaining individualsnot grpmax-eligible | 0.0145% | 6,906 |
| European (non-Finnish) | 0.004% | 25,012 |
| Admixed American | 0.00349% | 28,642 |
| East Asian | 0.00224% | 44,624 |
| South Asian | 0.00224% | 44,701 |
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
- TYROBP
- Protein
- p.Ser89=
- Coding
- c.267G>A
- MANE Select
- NM_003332
- dbSNP
- rs760509495
- Type
- single nucleotide variant
- Location
- chr19:35907227 (GRCh38)
- Gene constraint
- LOEUF 1.274 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 64.10 · 5 PDB
- Residue 89
- a UniProt-annotated variant site (found in patients with early-onset alzheimer disease; uncertain significance); the itam domain; the 'disordered' region
Similar variants
- TYROBP p.Ser89Leu Uncertain significance ★ ⚠ same residue
- TYROBP p.Ala44Thr Uncertain significance ★★ ⚠ same type
- TYROBP p.Arg70Trp Uncertain significance ★★ ⚠ same type
- TYROBP p.Asp104Asn Uncertain significance ★★ ⚠ same type
- TYROBP p.Asp32Asn Uncertain significance ★★ ⚠ same type
- TYROBP p.Pro40Leu Uncertain significance ★★ same type
- TYROBP p.Ser99Leu Uncertain significance ★★ ⚠ same type
- TYROBP p.Val38Met 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/tyrobp-p-ser89 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown