TGM2 p.Ser101=
c.303G>A · rs150909289 · VCV736016
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.109%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.41 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -13 | GERP -3.9 |
| Overall | ||
| CADD | 1.103 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.109%
European (non-Finnish) · 1,289/1,179,808 alleles
Filtering AF
0.104%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.102%
Overall
0.084%
1,356/1,613,340 alleles · rare
exomes 1,289/1,460,974 · genomes 67/152,366 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.109% | 915 |
| Remaining individualsnot grpmax-eligible | 0.032% | 3,123 |
| Admixed American | 0.0317% | 3,154 |
| Middle Eastern | 0.0165% | 6,052 |
| Finnishnot grpmax-eligible | 0.0141% | 7,099 |
| African / African-American | 0.012% | 8,341 |
| South Asian | 0.00771% | 12,970 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,566 |
| East Asian | 0.00223% | 44,860 |
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
- TGM2
- Protein
- p.Ser101=
- Coding
- c.303G>A
- MANE Select
- NM_004613
- dbSNP
- rs150909289
- Type
- single nucleotide variant
- Location
- chr20:38155977 (GRCh38)
- Gene constraint
- LOEUF 0.902 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.91 · 14 PDB
- Residue 101
- a β-strand
Similar variants
- TGM2 p.Ser101Leu Uncertain significance ★ ⚠ same residue
- TGM2 c.433+3G>A Likely benign ★★ same type
- TGM2 p.Ala282= Benign ★★ same type
- TGM2 p.Ala390= Benign ★★ same type
- TGM2 p.Arg28= Benign ★★ same type
- TGM2 p.Arg377His Benign ★★ ⚠ same type
- TGM2 p.Arg76His Benign ★★ same type
- TGM2 p.Asp326= Benign ★★ 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/tgm2-p-ser101 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown