SLMAP

protein-coding

sarcolemma 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

NM_001377540.1

Inheritance

AD

ClinVar variants

U:337B:192

Top phenotype

Brugada syndrome

gnomAD constraint

pLI —, LoF o/e 0.13

Max pathogenic AF

—

Genomic locus

chr3:57,755,450-57,930,003

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~174.6 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Brugada syndromeNO_KNOWN

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).

Brugada syndromeLIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0015263

Submitter: Genomics England PanelApp

Brugada syndromeSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0015263

Submitter: Orphanet

Brugada syndromeNO_KNOWN

Inheritance Pattern: AD

Disease ID:MONDO:0015263

Submitter: G2P

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SLMAP variants in ClinVar

6 Conditions Cataloged
Brugada syndromeTotal: 435
not specifiedTotal: 370
not providedTotal: 15
SLMAP-related disorderTotal: 11
Long QT syndromeTotal: 2
EBV-positive nodal T- and NK-cell lymphomaTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
177
clinvar
1
clinvar
179
missense
324
clinvar
14
clinvar
338
nonsense
1
clinvar
1
start loss
0
frameshift
3
clinvar
3
splice donor/acceptor (+/-2bp)
8
clinvar
8
Total003371911529
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 157 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001377540.1RefSeqNP_001364469.123MANE Select
ENST00000671191.1EnsemblENSP00000499458.123MANE Select
NM_001304420.3RefSeqNP_001291349.122Standard
NM_001304421.2RefSeqNP_001291350.120Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense1.703244220.7670.00002225326
Missense (PolyPhen)80141.030.567251799
Synonymous1.001381540.8970.000007971457
Loss of Function5.98754.70.1280.00000287645

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000120.00012rare
Latino/Admixed American0.000410.00040rare
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)0.0000540.000053rare
South Asian0.0000980.000098rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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