SPINT2 p.Arg182=
c.546C>T · rs201542510 · VCV1545086
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0396%, 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 -0.56 | GERP -0.9 |
| Overall | ||
| CADD | 7.653 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0396%
South Asian · 36/90,904 alleles
Filtering AF
0.0293%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0258%
Overall
0.0031%
50/1,611,770 alleles · ultra-rare
exomes 49/1,459,496 · genomes 1/152,274 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0396% | 2,525 |
| European (non-Finnish) | 0.00119% | 84,277 |
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
- SPINT2
- Protein
- p.Arg182=
- Coding
- c.546C>T
- MANE Select
- NM_021102
- dbSNP
- rs201542510
- Type
- single nucleotide variant
- Location
- chr19:38290273 (GRCh38)
- Gene constraint
- LOEUF 0.935 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.66 · 1 PDB
- Residue 182
- a UniProt-annotated variant site (in diar3; likely pathogenic); the bpti/kunitz inhibitor 2 domain
Similar variants
- SPINT2 p.Arg182Cys Uncertain significance ★★ ⚠ same residue
- SPINT2 p.Arg182His Uncertain significance ★★ ⚠ same residue
- SPINT2 p.Tyr163Cys Pathogenic ★★ same type
- SPINT2 p.Ala2Val Uncertain significance ★★ ⚠ same type
- SPINT2 p.Ala89Val Uncertain significance ★★ ⚠ same type
- SPINT2 p.Arg185Cys Uncertain significance ★★ ⚠ same type
- SPINT2 p.Arg225Gln Uncertain significance ★★ ⚠ same type
- SPINT2 p.Arg233Cys 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/spint2-p-arg182 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown