TDP2 p.Ser130Ter
c.389C>G · rs1562148727 · VCV620174
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 3 of 7 |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1.1 | GERP -3.5 |
| Overall | ||
| CADD | 33.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- TDP2
- Protein
- p.Ser130Ter
- Coding
- c.389C>G
- MANE Select
- NM_016614
- dbSNP
- rs1562148727
- Type
- single nucleotide variant
- Location
- chr6:24658597 (GRCh38)
- Gene constraint
- LOEUF 1.197 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.61 · 5 PDB
- Residue 130
- 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.Ser60= Likely benign ★★ same type
- TDP2 p.Arg317Ter 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-ser130ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown