TGM1 p.Arg71=
c.213A>G · rs2502509133 · VCV1999105
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
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. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.22 | GERP -2.5, phastCons 0.033 |
| Overall | ||
| CADD | 7.513 | 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
- TGM1
- Protein
- p.Arg71=
- Coding
- c.213A>G
- MANE Select
- NM_000359
- dbSNP
- rs2502509133
- Type
- single nucleotide variant
- Location
- chr14:24262140 (GRCh38)
- Gene constraint
- LOEUF 0.847 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 85.04 · 1 PDB
- Residue 71
- the 'membrane anchorage region' region; the 'disordered' region
Similar variants
- TGM1 p.Arg71Ter Pathogenic ★★ same residue
- TGM1 p.Arg71Gln Uncertain significance ★ ⚠ same residue
- TGM1 c.1159+1G>T Pathogenic ★★ same type
- TGM1 c.1645+1G>T Pathogenic/Likely pathogenic ★★ same type
- TGM1 c.2226-2A>G Pathogenic/Likely pathogenic ★★ same type
- TGM1 c.319+2T>C Likely pathogenic ★★ same type
- TGM1 c.876+2T>C Pathogenic/Likely pathogenic ★★ same type
- TGM1 c.877-2A>G 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/tgm1-p-arg71 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown