ITPR2 p.Val619=
c.1857C>T · VCV4916013
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.479%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>T here scores Δ0.93 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 5.6 | GERP 1.9, phastCons 1 |
| Overall | ||
| CADD | 11.4 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.479%
Middle Eastern · 29/6,056 alleles
Filtering AF
0.343%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.296%
Overall
0.115%
1,854/1,613,184 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.479% | 209 |
| Ashkenazi Jewishnot grpmax-eligible | 0.446% | 224 |
| Finnishnot grpmax-eligible | 0.15% | 666 |
| Remaining individualsnot grpmax-eligible | 0.149% | 672 |
| South Asian | 0.126% | 791 |
| European (non-Finnish) | 0.113% | 882 |
| Admixed American | 0.0567% | 1,764 |
| African / African-American | 0.0227% | 4,412 |
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.Val619=
- Coding
- c.1857C>T
- MANE Select
- NM_002223
- Type
- single nucleotide variant
- Location
- chr12:26659142 (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.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-val619 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown