TPSAB1 p.Pro103=
c.309G>A · VCV4927115
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 2.85%, afr)
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 -20 | GERP -3.4 |
| Overall | ||
| CADD | 5.831 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.85%
African / African-American · 1,931/67,670 alleles
Filtering AF
2.75%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.7%
Overall
1.25%
16,432/1,311,834 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.85% | 35 |
| Amishnot grpmax-eligible | 1.8% | 56 |
| European (non-Finnish) | 1.35% | 74 |
| Remaining individualsnot grpmax-eligible | 1.07% | 94 |
| Middle Eastern | 1.02% | 98 |
| Finnishnot grpmax-eligible | 0.958% | 104 |
| Ashkenazi Jewishnot grpmax-eligible | 0.712% | 140 |
| Admixed American | 0.425% | 236 |
| South Asian | 0.237% | 422 |
| East Asian | 0.00499% | 20,022 |
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
- TPSAB1
- Protein
- p.Pro103=
- Coding
- c.309G>A
- MANE Select
- NM_003294
- Type
- single nucleotide variant
- Location
- chr16:1241509 (GRCh38)
- Gene constraint
- LOEUF 1.9 · pLI <0.01 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 91.80 · 22 PDB
- Residue 103
- the peptidase s1 domain
Similar variants
- TPSAB1 p.Pro103Arg Uncertain significance ★ ⚠ same residue
- TPSAB1 p.Pro103Leu Uncertain significance ★ ⚠ same residue
- TPSAB1 p.Val76Met Uncertain significance ★★ same type
- TPSAB1 c.1-105C>A Benign ★★ same type
- TPSAB1 c.233+12G>A Benign ★★ same type
- TPSAB1 c.233+30G>C Benign ★★ same type
- TPSAB1 c.61+75T>C Benign ★★ same type
- TPSAB1 c.62-27C>T Benign ★★ 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/tpsab1-p-pro103 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown