TDP2 p.Ser60=
c.180C>T · rs190332937 · VCV731225
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.254%, 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 4.5 | GERP -0.15, phastCons 1 |
| Overall | ||
| CADD | 12.65 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.254%
East Asian · 114/44,888 alleles
Filtering AF
0.216%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.202%
Overall
0.00787%
127/1,614,222 alleles · rare
exomes 111/1,461,858 · genomes 16/152,364 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.254% | 394 |
| Remaining individualsnot grpmax-eligible | 0.008% | 12,502 |
| South Asian | 0.00659% | 15,181 |
| European (non-Finnish) | 0.000169% | 590,016 |
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
- TDP2
- Protein
- p.Ser60=
- Coding
- c.180C>T
- MANE Select
- NM_016614
- dbSNP
- rs190332937
- Type
- single nucleotide variant
- Location
- chr6:24666597 (GRCh38)
- Gene constraint
- LOEUF 1.197 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.61 · 5 PDB
- Residue 60
- an α-helix
Similar variants
- TDP2 p.Arg134Ter Pathogenic ★★ same type
- TDP2 p.Asn167= Likely benign ★★ same type
- TDP2 p.Asn59Asp Likely benign ★★ same type
- TDP2 p.Asn89Ser Benign/Likely benign ★★ same type
- TDP2 p.Leu28Val Benign/Likely benign ★★ same type
- TDP2 p.Pro348= Likely benign ★★ same type
- TDP2 p.Arg317Ter Pathogenic ★ same type
- TDP2 p.Ser130Ter Pathogenic ★ 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/tdp2-p-ser60 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown