EXOSC2 p.Thr45=
c.135G>A · rs550383127 · VCV1165148
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.708%, sas)
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 -4.9 | GERP -4.2 |
| Overall | ||
| CADD | 1.075 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.708%
South Asian · 645/91,082 alleles
Filtering AF
0.663%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.645%
Overall
0.0462%
745/1,614,058 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.708% | 141 |
| Middle Eastern | 0.115% | 866 |
| Remaining individualsnot grpmax-eligible | 0.048% | 2,084 |
| Admixed American | 0.00666% | 15,007 |
| European (non-Finnish) | 0.00475% | 21,070 |
| African / African-American | 0.004% | 25,013 |
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
- EXOSC2
- Protein
- p.Thr45=
- Coding
- c.135G>A
- MANE Select
- NM_014285
- dbSNP
- rs550383127
- Type
- single nucleotide variant
- Location
- chr9:130695504 (GRCh38)
- Gene constraint
- LOEUF 1.009 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.25 · 8 PDB
- Residue 45
- a β-strand
Similar variants
- EXOSC2 p.Thr45Met Uncertain significance ★ ⚠ same residue
- EXOSC2 p.Arg181Trp Uncertain significance ★★ ⚠ same type
- EXOSC2 p.Arg236Trp Uncertain significance ★★ ⚠ same type
- EXOSC2 p.Arg238Gln Uncertain significance ★★ ⚠ same type
- EXOSC2 p.Arg238Trp Uncertain significance ★★ ⚠ same type
- EXOSC2 p.Arg285Cys Uncertain significance ★★ ⚠ same type
- EXOSC2 p.Arg62Thr Uncertain significance ★★ same type
- EXOSC2 p.Arg87Leu 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/exosc2-p-thr45 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown