SLMAP
protein-codingsarcolemma associated protein, the group of STRIPAK complex
Gene summary
This gene encodes a component of a conserved striatin-interacting phosphatase and kinase complex. Striatin family complexes participate in a variety of cellular processes including signaling, cell cycle control, cell migration, Golgi assembly, and apoptosis. The protein encoded by this gene is a coiled-coil, tail-anchored membrane protein with a single C-terminal transmembrane domain that is posttranslationally inserted into membranes. Mutations in this gene are associated with Brugada syndrome, a cardiac channelopathy. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2015]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~174.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0015263
Submitter: ClinGen
SLMAP encodes the Sarcolemmal Membrane–Associated Protein, a protein initially purified from cardiac tissue and described to exist in three isoforms: SLMAP1 - 3 (PMID: 9405447). While the function of this gene is not well characterised, SLMAP has been implicated in biological processes such as muscle contraction (PMID: 30856349). Ishikawa et al. first suggested an association between SLMAP variants and autosomal dominant Brugada syndrome in 2012, following screening of a cohort of 190 Japanese patients (PMID: 23064965). Transfection of these variants in cell models resulted in decreased Nav1.5 surface expression and sodium current, prompting the authors to suggest a mechanism involving defective Nav1.5 trafficking. However, these variants are now known to be too common in the East Asian population to cause autosomal dominant Brugada syndrome. Since this initial report, there have been no further publications reporting SLMAP variants in the context of Brugada syndrome. There has only been one case report detailing a 20-year-old man who experienced a sudden death without clear cause and who carried a variant of unknown significance in SLMAP (p.Ser200Leu) (PMID: 34067575). Further, no rare SLMAP variants were identified by Di Resta et al. in their cohort of 91 patients with SCN5A-negative Brugada syndrome (PMID: 26220970). The cardiac overexpression of the SLMAP1-TM2 isoform in mice has been reported to cause ventricular dysfunction including a prolonged QT interval with dilation of the sarcoplasmic/endoplasmic reticulum (Nadar et al. PMID: 22180652). Additionally, the cardiac overexpression of SLMAP3 in mice was observed to cause systolic dysfunction with decreased fractional shortening, cardiac output and increased PR intervals (PMID: 30934005). The implication of these studies for the potential pathogenesis of SLMAP variants is unclear. SLMAP was originally classified as disputed for Brugada syndrome by the ClinGen Brugada Syndrome Gene Curation Expert Panel in 2017. This gene-disease relationship was re-evaluated on November 25, 2025, by the Hereditary Cardiovascular Disorders GCEP. Following re-evaluation, the gene-disease classification was refuted. This classification was approved by the ClinGen HCVD GCEP on November 25, 2025 (in accordance with SOP Version 11).
Inheritance Pattern: Unknown
Disease ID:MONDO:0015263
Submitter: Genomics England PanelApp
Inheritance Pattern: AD
Disease ID:MONDO:0015263
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0015263
Submitter: G2P
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to SLMAP variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001377540.1. 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 | 1 | 177 | 1 | 179 | ||
| missense | 324 | 14 | 338 | |||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 3 | 3 | ||||
| splice donor/acceptor (+/-2bp) | 8 | 8 | ||||
| Total | 0 | 0 | 337 | 191 | 1 | 529 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001364469.1 | 23 | MANE Select | |
| Ensembl | ENSP00000499458.1 | 23 | MANE Select | |
| RefSeq | NP_001291349.1 | 22 | Standard | |
| RefSeq | NP_001291350.1 | 20 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- muscle contraction
- protein localization to plasma membrane
- regulation of membrane depolarization during cardiac muscle cell action potential
- regulation of sodium ion transmembrane transport
- regulation of voltage-gated sodium channel activity
Molecular Function
- protein binding
Cellular Component
- smooth endoplasmic reticulum
- microtubule organizing center
- integral component of plasma membrane
- sarcolemma
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000295951
- Coding exons
- 21
- Length
- 173719
- Individuals with no LoFs
- 125717
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 25
- Defined
- 125742
- p
- 0.0000994
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.70 | 324 | 422 | 0.767 | 0.0000222 | 5326 |
| Missense (PolyPhen) | 80 | 141.03 | 0.56725 | 1799 | ||
| Synonymous | 1.00 | 138 | 154 | 0.897 | 0.00000797 | 1457 |
| Loss of Function | 5.98 | 7 | 54.7 | 0.128 | 0.00000287 | 645 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0.00041 | 0.00040 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000054 | 0.000053 | rare |
| South Asian | 0.000098 | 0.000098 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May play a role during myoblast fusion. {ECO:0000250}.;
Recessive Scores
- pRec
- 0.115
Intolerance Scores
- LoFtool
- 0.518
- RVIS EVS
- -1.16
- RVIS percentile EVS
- 6.17
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- E
- Indispensability pred.
- E
- Indispensability score
- 0.877
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |