SLN

sarcolipin

Basic information

Region (hg38): 11:107707378-107719693

Links

ENSG00000170290 ∙ NCBI:6588 ∙ OMIM:602203 ∙ HGNC:11089 ∙ Uniprot:O00631 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Transcripts

Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 8.

Transcript ID	Protein ID	Coding exons	MANE Select	MANE Plus Clinical
NM_003063.3	NP_003054.1	1	yes	-
ENST00000305991.3	ENSP00000304707.2	1	yes	-
ENST00000525934.1	ENSP00000434189.1	1	-	-
ENST00000531293.1	ENSP00000435380.1	1	-	-

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

• not_specified (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SLN gene is commonly pathogenic or not. These statistics are base on transcript: NM_003063.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			6			6
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	6	0	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SLN	protein_coding	protein_coding	ENST00000531293	1	12316

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.189	15	17.2	0.872	9.44e-7	197
Missense in Polyphen		2	2.4486	0.81678		23
Synonymous	0.300	6	7.01	0.856	3.86e-7	64
Loss of Function	0.233	0	0.0634	0.00	2.60e-9	1

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Reversibly inhibits the activity of ATP2A1 in sarcoplasmic reticulum by decreasing the apparent affinity of the ATPase for Ca(2+). Modulates calcium re-uptake during muscle relaxation and plays an important role in calcium homeostasis in muscle. Required for muscle-based, non-shivering thermogenesis (By similarity). {ECO:0000250|UniProtKB:Q9CQD6, ECO:0000269|PubMed:11781085, ECO:0000269|PubMed:9575189}.
• Pathway: Ion channel transport;Ion homeostasis;Transport of small molecules;Cardiac conduction;Muscle contraction;Ion transport by P-type ATPases (Consensus)

Intolerance Scores

• rvis_EVS: 0.08
• rvis_percentile_EVS: 59.43

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Low	Low	Low
Primary Immunodeficiency	Low	Low	Low
Cancer	Low	Low	Low

Gene ontology

• Biological process: calcium ion transport;negative regulation of catalytic activity;negative regulation of protein complex disassembly;regulation of calcium ion transport;sarcoplasmic reticulum calcium ion transport;negative regulation of calcium ion import;positive regulation of cold-induced thermogenesis;negative regulation of calcium ion transmembrane transporter activity;regulation of relaxation of muscle;negative regulation of calcium ion binding;positive regulation of protein depolymerization;regulation of calcium-transporting ATPase activity
• Cellular component: integral component of membrane;sarcoplasmic reticulum;sarcoplasmic reticulum membrane
• Molecular function: enzyme inhibitor activity;protein binding;ATPase binding