MTPAP p.Pro473=
c.1419T>C · rs17855115 · VCV2135597
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00133%, afr)
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 · A>C here scores Δ0.26 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.4 | GERP -3.6 |
| Overall | ||
| CADD | 3.511 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00133%
African / African-American · 1/75,042 alleles
Overall
6.2e-05%
1/1,613,970 alleles · very rare
exomes 1/1,461,650 · genomes 0/152,320 · joint denominator
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
- MTPAP
- Protein
- p.Pro473=
- Coding
- c.1419T>C
- MANE Select
- NM_018109
- dbSNP
- rs17855115
- Type
- single nucleotide variant
- Location
- chr10:30313939 (GRCh38)
- Gene constraint
- LOEUF 0.641 · pLI 0.03 (gnomAD)
- Structure
- AlphaFold pLDDT 83.16 · 1 PDB
- Residue 473
- the pap-associated domain
Similar variants
- MTPAP p.Asn478Asp Pathogenic ★★ ⚠ same type
- MTPAP p.Ala141Thr Uncertain significance ★★ ⚠ same type
- MTPAP p.Ala219Thr Uncertain significance ★★ ⚠ same type
- MTPAP p.Arg160Trp Uncertain significance ★★ ⚠ same type
- MTPAP p.Arg171Cys Uncertain significance ★★ ⚠ same type
- MTPAP p.Arg461Gln Uncertain significance ★★ ⚠ same type
- MTPAP p.Arg76Gln Uncertain significance ★★ ⚠ same type
- MTPAP p.Asn129Ser 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/mtpap-p-pro473 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown