TPM2 p.Ser87=
c.261C>G · VCV3680394
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
arthrogryposis, distal, type 1A
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 1.1 | GERP -2.8, phastCons 1 |
| Overall | ||
| CADD | 7.81 | PHRED · no single calibrated threshold — expert panels disagree |
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
- TPM2
- Protein
- p.Ser87=
- Coding
- c.261C>G
- MANE Select
- NM_003289
- Type
- single nucleotide variant
- Location
- chr9:35685760 (GRCh38)
- Gene constraint
- LOEUF 0.87 · pLI <0.01 · ClinGen HI 1/3 (gnomAD)
- Structure
- AlphaFold pLDDT 91.51
- Residue 87
- a modified residue (phosphoserine)
Similar variants
- TPM2 p.Ala155Thr Pathogenic/Likely pathogenic ★★ same condition
- TPM2 p.Arg133Trp Pathogenic ★★ same condition
- TPM2 p.Gln24Ter Pathogenic/Likely pathogenic ★★ same condition
- TPM2 p.Gln9Pro Likely pathogenic ★★ same condition
- TPM2 p.Glu117Lys Pathogenic/Likely pathogenic ★★ same condition
- TPM2 p.Lys128Glu Likely pathogenic ★★ same condition
- TPM2 p.Tyr261Cys Pathogenic/Likely pathogenic ★★ same condition
- TPM2 c.240+5G>T Uncertain significance ★★ same condition
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/tpm2-p-ser87 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown