GRAMD2A
protein-codingGRAM domain containing 2A, the group of GRAM domain containing
Gene summary
Enables phosphatidylinositol binding activity and phosphatidylinositol-4,5-bisphosphate binding activity. Involved in endoplasmic reticulum-plasma membrane tethering and regulation of store-operated calcium entry. Located in endoplasmic reticulum membrane; organelle membrane contact site; and plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]
- GRAMD2
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~38.0 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 GRAMD2A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001012642.3. 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 | 0 | |||||
| missense | 46 | 2 | 48 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 49 | 3 | 0 | 52 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001012660.1 | 12 | MANE Select | |
| Ensembl | ENSP00000311657.7 | 12 | MANE Select | |
| Ensembl | ENSP00000457155.1 | 3 | Standard | |
| Ensembl | ENSP00000457660.1 | 9 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- endoplasmic reticulum-plasma membrane tethering
- regulation of store-operated calcium entry
Molecular Function
- phosphatidylinositol-4,5-bisphosphate binding
- phosphatidylinositol binding
Cellular Component
- integral component of membrane
- intrinsic component of endoplasmic reticulum membrane
- extrinsic component of cytoplasmic side of plasma membrane
- organelle membrane contact site
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000309731
- Coding exons
- 12
- Length
- 37979
- Individuals with no LoFs
- 125305
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 442
- Defined
- 125748
- p
- 0.00176
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.959 | 149 | 186 | 0.802 | 0.00000945 | 2303 |
| Missense (PolyPhen) | 51 | 68.612 | 0.74332 | 824 | ||
| Synonymous | 1.41 | 55 | 70.0 | 0.786 | 0.00000329 | 664 |
| Loss of Function | 0.281 | 20 | 21.4 | 0.934 | 9.92e-7 | 259 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00056 | 0.00055 | rare |
| Latino/Admixed American | 0.00060 | 0.00055 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.0016 | 0.0016 | notable |
| Finnish | 0.0011 | 0.0011 | notable |
| European (Non-Finnish) | 0.0029 | 0.0028 | notable |
| South Asian | 0.00087 | 0.00085 | rare |
| Other | 0.0025 | 0.0024 | notable |
dbNSFP Gene Annotations
Source:
Intolerance Scores
- RVIS EVS
- 0.35
- RVIS percentile EVS
- 74.37
Essentials
- Essential (gene trap)
- N