ITPRID2
protein-codingITPR interacting domain containing 2
Gene summary
Enables actin filament binding activity. Located in cytosol. [provided by Alliance of Genome Resources, Jun 2026]
- SSFA2
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~39.0 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to ITPRID2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001130445.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 2 | ||||
| missense | 208 | 5 | 213 | |||
| nonsense | 2 | 2 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 6 | 6 | ||||
| Total | 0 | 0 | 218 | 5 | 0 | 223 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001123917.1 | 17 | MANE Select | |
| Ensembl | ENSP00000388731.2 | 17 | MANE Select | |
| RefSeq | NP_001274432.1 | 16 | Standard | |
| RefSeq | NP_001274433.1 | 11 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Molecular Function
- signaling receptor binding
- actin filament binding
Cellular Component
- nucleus
- cytosol
- plasma membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000431877
- Coding exons
- 17
- Length
- 38906
- Individuals with no LoFs
- 125692
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 56
- Defined
- 125748
- p
- 0.000223
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.408 | 697 | 667 | 1.04 | 0.0000339 | 8207 |
| Missense (PolyPhen) | 279 | 296.93 | 0.93963 | 3741 | ||
| Synonymous | 0.667 | 229 | 242 | 0.945 | 0.0000122 | 2460 |
| Loss of Function | 4.29 | 21 | 55.5 | 0.378 | 0.00000283 | 721 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0.00021 | 0.00020 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.00060 | 0.00060 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00023 | 0.00023 | rare |
| South Asian | 0.00026 | 0.00026 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.100
Intolerance Scores
- RVIS EVS
- 0.24
- RVIS percentile EVS
- 68.6
Essentials
- Essential (gene trap)
- N