AGTPBP1 p.Arg2Pro
c.5G>C · VCV4075555
Uncertain significance
Single submitter
Classification
Uncertain significance
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. | ||
| REVEL | 0.065 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Pangolin | Δ0.21 | gain · loss 0.00 · not in the SpliceAI release · independent |
| Constraint at this position | ||
| Conservation | phyloP 0.084 | GERP -0.14, phastCons 0.57 |
| Overall | ||
| CADD | 15.25 | 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
- AGTPBP1
- Protein
- p.Arg2Pro
- Coding
- c.5G>C
- MANE Select
- NM_001330701 · reported on NM_001286715
- Type
- single nucleotide variant
- Location
- chr9:85741958 (GRCh38)
- Gene constraint
- LOEUF 0.556 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.95
Similar variants
- AGTPBP1 p.Ser2Asn Uncertain significance ★ ⚠ same residue
- AGTPBP1 c.-206G>A Uncertain significance ★★ same type
- AGTPBP1 p.Ala461Gly Uncertain significance ★★ ⚠ same type
- AGTPBP1 p.Arg1136His Uncertain significance ★★ ⚠ same type
- AGTPBP1 p.Arg174His Uncertain significance ★★ ⚠ same type
- AGTPBP1 p.Cys1069Phe Uncertain significance ★★ ⚠ same type
- AGTPBP1 p.Glu1176Gly Uncertain significance ★★ ⚠ same type
- AGTPBP1 c.-87T>C Benign/Likely 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/agtpbp1-p-arg2pro (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown