ITPR2 p.Pro165=
c.495G>A · rs34506525 · VCV3037589
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.507%, afr)
Conditions
1
ITPR2-related disorder
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 0.15 | GERP -0.18, phastCons 0.79 |
| Overall | ||
| CADD | 12.68 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.507%
African / African-American · 380/74,934 alleles
Filtering AF
0.465%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.448%
Overall
0.027%
436/1,612,148 alleles · rare
exomes 221/1,459,894 · genomes 215/152,254 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.507% | 197 |
| Admixed American | 0.0384% | 2,604 |
| Remaining individualsnot grpmax-eligible | 0.0305% | 3,284 |
| Middle Eastern | 0.0165% | 6,046 |
| South Asian | 0.0033% | 30,259 |
| East Asian | 0.00223% | 44,802 |
| European (non-Finnish) | 0.000763% | 130,990 |
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.Pro165=
- Coding
- c.495G>A
- MANE Select
- NM_002223
- dbSNP
- rs34506525
- Type
- single nucleotide variant
- Location
- chr12:26722427 (GRCh38)
- Gene constraint
- LOEUF 0.724 · pLI <0.01 (gnomAD)
- Residue 165
- the mir 1 domain
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.Glu815= 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-pro165 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown