ITPR3 p.Pro796=
c.2388G>A · rs17526232 · VCV1235627
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 10.5%, sas) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -20 | GERP -5 |
| Overall | ||
| CADD | 0.095 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
10.5%
South Asian · 9,526/91,072 alleles
Filtering AF
10.3%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 10.2%
Overall
1.76%
28,439/1,613,698 alleles · common
exomes 26,141/1,461,608 · genomes 2,298/152,090 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 10.5% | 10 |
| Finnishnot grpmax-eligible | 4.33% | 23 |
| East Asian | 4.17% | 24 |
| Middle Eastern | 3.32% | 30 |
| Remaining individualsnot grpmax-eligible | 2.36% | 42 |
| European (non-Finnish) | 1.01% | 99 |
| Admixed American | 0.655% | 153 |
| Ashkenazi Jewishnot grpmax-eligible | 0.345% | 290 |
| Amishnot grpmax-eligible | 0.329% | 304 |
| African / African-American | 0.223% | 449 |
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
- ITPR3
- Protein
- p.Pro796=
- Coding
- c.2388G>A
- MANE Select
- NM_002224
- dbSNP
- rs17526232
- Type
- single nucleotide variant
- Location
- chr6:33670523 (GRCh38)
- Gene constraint
- LOEUF 0.67 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.04 · 24 PDB
Similar variants
- ITPR3 p.Thr1424Met Pathogenic/Likely pathogenic ★★ ⚠ same type
- ITPR3 p.Ala1352Thr Uncertain significance ★★ ⚠ same type
- ITPR3 p.Arg1085Leu Uncertain significance ★★ ⚠ same type
- ITPR3 p.Arg2659Cys Uncertain significance ★★ ⚠ same type
- ITPR3 p.Asp1968Val Uncertain significance ★★ ⚠ same type
- ITPR3 p.Glu669Asp Uncertain significance ★★ ⚠ same type
- ITPR3 p.Gly1008Trp Uncertain significance ★★ ⚠ same type
- ITPR3 p.Gly2514Glu 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/itpr3-p-pro796 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown