TSEN34 p.Pro72=
c.216G>T · rs530821643 · VCV1939969
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0781%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.1 | GERP -0.079, phastCons 1 |
| Overall | ||
| CADD | 12.07 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0781%
East Asian · 35/44,814 alleles
Filtering AF
0.0577%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0507%
Overall
0.00231%
37/1,602,726 alleles · ultra-rare
exomes 36/1,450,530 · genomes 1/152,196 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0781% | 1,280 |
| Finnishnot grpmax-eligible | 0.00187% | 53,432 |
| European (non-Finnish) | 8.48e-05% | 1,179,504 |
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
- TSEN34
- Protein
- p.Pro72=
- Coding
- c.216G>T
- MANE Select
- NM_001077446
- dbSNP
- rs530821643
- Type
- single nucleotide variant
- Location
- chr19:54191580 (GRCh38)
- Gene constraint
- LOEUF 1.159 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 84.74 · 6 PDB
- Residue 72
- an α-helix
Similar variants
- TSEN34 p.Pro72Ala Uncertain significance ★ ⚠ same residue
- TSEN34 p.Arg253His Uncertain significance ★★ ⚠ same type
- TSEN34 p.Arg25Cys Uncertain significance ★★ ⚠ same type
- TSEN34 p.Arg88Cys Uncertain significance ★★ ⚠ same type
- TSEN34 p.Asp148Tyr Uncertain significance ★★ ⚠ same type
- TSEN34 p.Gly39Arg Uncertain significance ★★ ⚠ same type
- TSEN34 p.Ile116Phe Uncertain significance ★★ ⚠ same type
- TSEN34 p.Leu227Val Uncertain significance ★★ ⚠ 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/tsen34-p-pro72 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown