SLMAP

sarcolemma associated protein, the group of STRIPAK complex

Basic information

Region (hg38): 3:57755449-57930003

Links

ENSG00000163681 ∙ NCBI:7871 ∙ OMIM:602701 ∙ HGNC:16643 ∙ Uniprot:Q14BN4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Brugada syndrome (Limited), mode of inheritance: Unknown
• Brugada syndrome (Supportive), mode of inheritance: AD
• Brugada syndrome (Disputed Evidence), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SLMAP gene.

• Brugada syndrome (313 variants)
• Inborn genetic diseases (179 variants)
• not provided (26 variants)
• not specified (8 variants)
• Long QT syndrome (2 variants)
• Cardiac arrest (1 variants)
• SLMAP-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLMAP gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	124	2	127
missense			180	7		187
nonsense				1		1
start loss						0
frameshift			1			1
inframe indel			2	1		3
splice donor/acceptor (+/-2bp)			4			4
splice region			16	17	2	35
non coding				34	33	67
Total	0	0	188	167	35

Variants in SLMAP

This is a list of pathogenic ClinVar variants found in the SLMAP region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-57757519-G-A			Benign (Apr 04, 2019)
3-57757610-C-C		not specified	Likely benign (Aug 02, 2017)
3-57757655-C-T		Brugada syndrome	Uncertain significance (Jun 14, 2019)
3-57757660-A-T		not specified	Likely benign (Nov 25, 2023)
3-57757663-C-T		not specified	Likely benign (May 27, 2021)
3-57757682-C-T		Brugada syndrome	Uncertain significance (Aug 21, 2021)
3-57757684-C-G		not specified	Likely benign (Nov 15, 2021)
3-57757693-G-T		Brugada syndrome • not specified	Likely benign (Sep 24, 2020)
3-57757699-G-A		Brugada syndrome	Likely benign (Aug 16, 2022)
3-57757713-A-G		not specified	Uncertain significance (May 27, 2023)
3-57757721-C-T		Brugada syndrome	Likely benign (Jun 13, 2022)
3-57757723-G-C		Brugada syndrome • not specified	Likely benign (May 31, 2021)
3-57757726-C-T		Brugada syndrome • not specified	Likely benign (Dec 30, 2022)
3-57757735-C-T		not specified	Likely benign (Nov 15, 2021)
3-57757741-C-T		not specified	Likely benign (Nov 15, 2021)
3-57757744-C-T		Brugada syndrome • not specified	Likely benign (Feb 22, 2020)
3-57757750-A-C		not specified	Likely benign (Nov 15, 2021)
3-57757762-T-C		Brugada syndrome	Likely benign (Nov 14, 2022)
3-57757764-G-T		Brugada syndrome	Uncertain significance (Feb 28, 2022)
3-57757770-C-T		Brugada syndrome	Uncertain significance (Jul 13, 2021)
3-57757801-G-A		Brugada syndrome	Likely benign (May 10, 2022)
3-57757802-C-G		not specified	Uncertain significance (Jun 23, 2021)
3-57757802-C-T		not specified	Likely benign (Oct 08, 2023)
3-57757804-A-G		Brugada syndrome • not specified	Likely benign (Jan 31, 2024)
3-57757813-C-T		not specified	Likely benign (Aug 05, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLMAP	protein_coding	protein_coding	ENST00000295951	21	173719

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000238	125717	0	25	125742	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.70	324	422	0.767	0.0000222	5326
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000532	0.000531
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000538	0.0000527
Middle Eastern	0.00	0.00
South Asian	0.0000982	0.0000980
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.431
• hipred: Y
• hipred_score: 0.683
• ghis: 0.661

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.877

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Slmap
• Phenotype: digestive/alimentary phenotype; growth/size/body region phenotype; craniofacial phenotype

Gene ontology

• 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
• Cellular component: smooth endoplasmic reticulum;microtubule organizing center;integral component of plasma membrane;sarcolemma
• Molecular function: protein binding