ITPR2 p.Asn461=
c.1383C>T · rs35412320 · VCV717312
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.05%, afr)
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 -5.9 | GERP -3.4 |
| Overall | ||
| CADD | 0.976 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.05%
African / African-American · 2,284/74,934 alleles
Filtering AF
2.94%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.9%
Overall
0.158%
2,548/1,612,128 alleles · low-frequency
exomes 1,227/1,459,932 · genomes 1,321/152,196 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.05% | 33 |
| Remaining individualsnot grpmax-eligible | 0.186% | 538 |
| Admixed American | 0.154% | 651 |
| Middle Eastern | 0.0661% | 1,513 |
| South Asian | 0.0044% | 22,726 |
| European (non-Finnish) | 0.00399% | 25,078 |
| East Asian | 0.00223% | 44,854 |
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.Asn461=
- Coding
- c.1383C>T
- MANE Select
- NM_002223
- dbSNP
- rs35412320
- Type
- single nucleotide variant
- Location
- chr12:26681900 (GRCh38)
- Gene constraint
- LOEUF 0.724 · pLI <0.01 (gnomAD)
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.Asp1413= 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-asn461 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown