MTPAP p.Val115=
c.345C>T · rs548128535 · VCV1256275
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.254%, 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 0.35 | GERP -2.9, phastCons 0.56 |
| Overall | ||
| CADD | 6.233 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.254%
South Asian · 231/91,052 alleles
Filtering AF
0.227%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.216%
Overall
0.0182%
294/1,613,636 alleles · rare
exomes 279/1,461,478 · genomes 15/152,158 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.254% | 394 |
| East Asian | 0.0379% | 2,640 |
| Remaining individualsnot grpmax-eligible | 0.0272% | 3,676 |
| Middle Eastern | 0.0165% | 6,062 |
| Admixed American | 0.00833% | 11,998 |
| African / African-American | 0.008% | 12,498 |
| European (non-Finnish) | 0.00144% | 69,393 |
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.Val115=
- Coding
- c.345C>T
- MANE Select
- NM_018109
- dbSNP
- rs548128535
- Type
- single nucleotide variant
- Location
- chr10:30340436 (GRCh38)
- Gene constraint
- LOEUF 0.641 · pLI 0.03 (gnomAD)
- Structure
- AlphaFold pLDDT 83.16 · 1 PDB
- Residue 115
- a β-strand
Similar variants
- MTPAP p.Val115Ile 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-val115 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown