ITPR2 p.Ser1289=
c.3867C>T · rs201711868 · VCV725613
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.252%, afr)
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 -2.7 | GERP -5.5 |
| Overall | ||
| CADD | 5.583 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.252%
African / African-American · 189/75,022 alleles
Filtering AF
0.223%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.211%
Overall
0.0127%
205/1,614,002 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.252% | 397 |
| Remaining individualsnot grpmax-eligible | 0.0096% | 10,417 |
| South Asian | 0.00329% | 30,361 |
| Admixed American | 0.00167% | 60,004 |
| European (non-Finnish) | 0.000509% | 196,652 |
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.Ser1289=
- Coding
- c.3867C>T
- MANE Select
- NM_002223
- dbSNP
- rs201711868
- Type
- single nucleotide variant
- Location
- chr12:26599280 (GRCh38)
- Gene constraint
- LOEUF 0.724 · pLI <0.01 (gnomAD)
Similar variants
- ITPR2 p.Ser1289Asn Uncertain significance ★ ⚠ same residue
- 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
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-ser1289 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown