MTPAP p.Ser337=
c.1011C>T · rs139195646 · VCV1256274
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0278%, nfe)
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 -0.45 | GERP -3.9, phastCons 0.001 |
| Overall | ||
| CADD | 5.416 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0278%
European (non-Finnish) · 328/1,178,944 alleles
Filtering AF
0.0253%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0243%
Overall
0.0214%
345/1,612,534 alleles · ultra-rare
exomes 325/1,460,430 · genomes 20/152,104 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0278% | 3,594 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,938 |
| African / African-American | 0.00801% | 12,485 |
| East Asian | 0.00223% | 44,860 |
| South Asian | 0.0011% | 90,990 |
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.Ser337=
- Coding
- c.1011C>T
- MANE Select
- NM_018109
- dbSNP
- rs139195646
- Type
- single nucleotide variant
- Location
- chr10:30322599 (GRCh38)
- Gene constraint
- LOEUF 0.641 · pLI 0.03 (gnomAD)
- Structure
- AlphaFold pLDDT 83.16 · 1 PDB
- Residue 337
- an α-helix
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-ser337 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown