PALM
protein-codingparalemmin, the group of Paralemmins
Gene summary
This gene encodes a member of the paralemmin protein family. The product of this gene is a prenylated and palmitoylated phosphoprotein that associates with the cytoplasmic face of plasma membranes and is implicated in plasma membrane dynamics in neurons and other cell types. Several alternatively spliced transcript variants have been identified, but the full-length nature of only two transcript variants has been determined. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~39.4 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 PALM variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_002579.3. 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 | 53 | 9 | 62 | |||
| missense | 137 | 9 | 2 | 148 | ||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 141 | 62 | 11 | 214 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_002570.2 | 9 | MANE Select | |
| Ensembl | ENSP00000341911.4 | 9 | MANE Select | |
| RefSeq | NP_001035224.1 | 8 | Standard | |
| Ensembl | ENSP00000264560.7 | 8 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- cytoskeleton organization
- adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway
- negative regulation of adenylate cyclase activity
- regulation of cell shape
- positive regulation of filopodium assembly
Molecular Function
- protein binding
- D3 dopamine receptor binding
Cellular Component
- nucleus
- plasma membrane
- postsynaptic density
- basolateral plasma membrane
- apicolateral plasma membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000338448
- Coding exons
- 9
- Length
- 39377
- Individuals with no LoFs
- 102192
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 1
- Defined
- 102193
- p
- 0.00000489
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.716 | 223 | 255 | 0.874 | 0.0000180 | 2445 |
| Missense (PolyPhen) | 63 | 74.991 | 0.8401 | 721 | ||
| Synonymous | -1.70 | 144 | 120 | 1.20 | 0.00000980 | 796 |
| Loss of Function | 2.87 | 3 | 15.0 | 0.200 | 6.40e-7 | 190 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000011 | 0.000011 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Involved in plasma membrane dynamics and cell process formation. Isoform 1 and isoform 2 are necessary for axonal and dendritic filopodia induction, for dendritic spine maturation and synapse formation in a palmitoylation-dependent manner. {ECO:0000269|PubMed:14978216}.;
Recessive Scores
- pRec
- 0.108
Intolerance Scores
- LoFtool
- 0.270
- RVIS EVS
- -0.78
- RVIS percentile EVS
- 12.97
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.237
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |