MTPAP p.Arg503fs
c.1507del · VCV4682196
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
frameshift
predicted LoF
gnomAD v4.1
Rare
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | frameshift | predicted loss-of-function |
|---|---|---|
| NMD | escapes | premature termination codon in the last exon (9 of 9) — the truncated protein is likely expressed. PVS1 input, not an applied code |
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 1.8 | GERP -0.059, phastCons 1 |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Variant & gene context
- Gene
- MTPAP
- Protein
- p.Arg503fs
- Coding
- c.1507del
- MANE Select
- NM_018109
- Type
- Deletion
- Location
- chr10:30313851 (GRCh38)
- Gene constraint
- LOEUF 0.641 · pLI 0.03 (gnomAD)
- Structure
- AlphaFold pLDDT 83.16 · 1 PDB
- Residue 503
- an α-helix
Similar variants
- MTPAP p.Arg503Gln Likely benign ★ same residue
- MTPAP c.1312+3_1312+6del Uncertain significance ★ same type
- MTPAP c.1313-29_1313-13del Uncertain significance ★ same type
- MTPAP p.Ser546fs Uncertain significance ★ same type
- MTPAP p.Thr572fs Uncertain significance ★ same type
- MTPAP p.Val78_Leu79insTer Uncertain significance ★ same type
- MTPAP c.1386+114del Benign ★ same type
- MTPAP c.331-19_331-8del 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/mtpap-p-arg503fs (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown