MTPAP p.Ser320=
c.960C>T · rs185764766 · VCV381066
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.147%, eas)
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 -0.19 | GERP -2.3, phastCons 0.002 |
| Overall | ||
| CADD | 11.56 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.147%
East Asian · 66/44,886 alleles
Filtering AF
0.119%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.108%
Overall
0.00582%
94/1,613,996 alleles · rare
exomes 90/1,461,834 · genomes 4/152,162 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.147% | 680 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,835 |
| European (non-Finnish) | 0.00195% | 51,304 |
| African / African-American | 0.00133% | 75,008 |
| South Asian | 0.0011% | 91,066 |
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.Ser320=
- Coding
- c.960C>T
- MANE Select
- NM_018109
- dbSNP
- rs185764766
- Type
- single nucleotide variant
- Location
- chr10:30326456 (GRCh38)
- Gene constraint
- LOEUF 0.641 · pLI 0.03 (gnomAD)
- Structure
- AlphaFold pLDDT 83.16 · 1 PDB
- Residue 320
- a turn
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-ser320 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown