ITPR1 p.Ser366del
c.1093TCC[1] · rs746446105 · VCV2274956
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.48e-05%, nfe)
Conditions
1
Inborn genetic diseases
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 7.8 | GERP 2, phastCons 1 |
| Overall | ||
| CADD | 19.08 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.48e-05%
European (non-Finnish) · 1/1,179,706 alleles
Overall
6.2e-05%
1/1,613,566 alleles · very rare
exomes 0/1,461,482 · genomes 1/152,084 · joint denominator
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
- ITPR1
- Protein
- p.Ser366del
- Coding
- c.1093TCC[1]
- MANE Select
- NM_001378452
- dbSNP
- rs746446105
- Type
- Microsatellite
- Location
- chr3:4658219 (GRCh38)
- Gene constraint
- LOEUF 0.325 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
- Residue 366
- the mir 4 domain
Similar variants
- ITPR1 p.Leu605Phe Likely pathogenic ★★ same condition
- ITPR1 p.Thr2434Ile Likely pathogenic ★★ same condition
- ITPR1 c.1554+4G>A Uncertain significance ★★ same condition
- ITPR1 c.3564+5G>T Uncertain significance ★★ same condition
- ITPR1 p.Ala1222Thr Uncertain significance ★★ ⚠ same condition
- ITPR1 p.Ala1222Val Uncertain significance ★★ same condition
- ITPR1 p.Ala1480Thr Uncertain significance ★★ same condition
- ITPR1 p.Ala1743Val Uncertain significance ★★ 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/itpr1-p-ser366del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown