MTPAP p.Pro46=
c.138T>C · rs147352132 · VCV743121
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.192%, sas)
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 -0.7 | GERP -3.6 |
| Overall | ||
| CADD | 4.23 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.192%
South Asian · 175/91,062 alleles
Filtering AF
0.169%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.16%
Overall
0.0432%
697/1,613,838 alleles · rare
exomes 647/1,461,672 · genomes 50/152,166 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.192% | 520 |
| Ashkenazi Jewishnot grpmax-eligible | 0.105% | 955 |
| Finnishnot grpmax-eligible | 0.0562% | 1,778 |
| Remaining individualsnot grpmax-eligible | 0.056% | 1,785 |
| European (non-Finnish) | 0.0342% | 2,920 |
| Middle Eastern | 0.033% | 3,028 |
| African / African-American | 0.012% | 8,333 |
| Admixed American | 0.00834% | 11,998 |
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.Pro46=
- Coding
- c.138T>C
- MANE Select
- NM_018109
- dbSNP
- rs147352132
- Type
- single nucleotide variant
- Location
- chr10:30349138 (GRCh38)
- Gene constraint
- LOEUF 0.641 · pLI 0.03 (gnomAD)
- Structure
- AlphaFold pLDDT 83.16 · 1 PDB
Similar variants
- MTPAP p.Pro46Thr Uncertain significance ★★ ⚠ same residue
- 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
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-pro46 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown