ITPR2 p.Glu815=
c.2445A>G · rs765580395 · VCV3050840
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.348%, mid)
Conditions
1
ITPR2-related disorder
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 -0.64 | GERP 0.7, phastCons 0.045 |
| Overall | ||
| CADD | 7.255 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.348%
Middle Eastern · 21/6,040 alleles
Filtering AF
0.233%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.196%
Overall
0.00249%
40/1,605,962 alleles · rare
exomes 33/1,453,660 · genomes 7/152,302 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.348% | 288 |
| Remaining individualsnot grpmax-eligible | 0.00643% | 15,562 |
| Admixed American | 0.0017% | 58,702 |
| African / African-American | 0.00134% | 74,612 |
| European (non-Finnish) | 0.0011% | 90,535 |
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
- ITPR2
- Protein
- p.Glu815=
- Coding
- c.2445A>G
- MANE Select
- NM_002223
- dbSNP
- rs765580395
- Type
- single nucleotide variant
- Location
- chr12:26655852 (GRCh38)
- Gene constraint
- LOEUF 0.724 · pLI <0.01 (gnomAD)
Disease context
ITPR2-related disorder
Similar variants
- ITPR2 c.279+6G>C Benign same condition
- ITPR2 c.3122+4T>C Likely benign same condition
- ITPR2 c.3552+3C>T Likely benign same condition
- ITPR2 c.4381-8C>T Likely benign same condition
- ITPR2 p.Ala2112= Likely benign same condition
- ITPR2 p.Ala898= Benign same condition
- ITPR2 p.Asp2103= Likely benign same condition
- ITPR2 p.Phe1958= Likely benign same condition
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/itpr2-p-glu815 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown