ITPR2 p.Ile431=
c.1293C>T · VCV4916014
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.446%, mid)
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 -1.1 | GERP -3.4 |
| Overall | ||
| CADD | 2.905 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.446%
Middle Eastern · 27/6,060 alleles
Filtering AF
0.402%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.387%
Overall
0.039%
629/1,613,586 alleles · rare
exomes 393/1,461,264 · genomes 236/152,322 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.446% | 224 |
| African / African-American | 0.441% | 227 |
| Admixed American | 0.108% | 923 |
| Remaining individualsnot grpmax-eligible | 0.0816% | 1,225 |
| Ashkenazi Jewishnot grpmax-eligible | 0.027% | 3,698 |
| European (non-Finnish) | 0.0121% | 8,249 |
| East Asian | 0.00446% | 22,438 |
| South Asian | 0.0022% | 45,516 |
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.Ile431=
- Coding
- c.1293C>T
- MANE Select
- NM_002223
- Type
- single nucleotide variant
- Location
- chr12:26681990 (GRCh38)
- Gene constraint
- LOEUF 0.724 · pLI <0.01 (gnomAD)
- Residue 431
- the mir 5 domain
Similar variants
- ITPR2 p.Val1162Gly Uncertain significance ★★ same type
- ITPR2 c.3801+23G>A Benign ★★ same type
- ITPR2 c.5073+10T>A Benign ★★ same type
- ITPR2 c.93-10T>A Benign ★★ same type
- ITPR2 p.Ala1898Val Benign ★★ same type
- ITPR2 p.Arg1180Gln Likely benign ★★ same type
- ITPR2 p.Arg1275Gln Likely benign ★★ same type
- ITPR2 p.Asn461= 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/itpr2-p-ile431 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown