SGCE

sarcoglycan epsilon

Basic information

Region (hg38): 7:94524204-94656572

Previous symbols: [ "DYT11" ]

Links

ENSG00000127990 ∙ NCBI:8910 ∙ OMIM:604149 ∙ HGNC:10808 ∙ Uniprot:O43556 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• myoclonic dystonia 11 (Strong), mode of inheritance: AD
• myoclonus-dystonia syndrome (Supportive), mode of inheritance: AD
• myoclonic dystonia 11 (Definitive), mode of inheritance: AD
• myoclonic dystonia 11 (Strong), mode of inheritance: AD
• myoclonic dystonia 11 (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Dystonia 11, myoclonic	AD	Neurologic	Treatment with deep-brain stimulation may be beneficial	Musculoskeletal; Neurologic	4434166; 11528394; 12325078; 12391346; 11912106; 12634861; 12821748; 12743249; 16240355; 15728306; 17101905; 16534121; 16227522; 18362280; 20301587; 20800530; 21220679; 21267590; 21825253; 22026499

ClinVar

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

• Myoclonic dystonia 11 (82 variants)
• not provided (29 variants)
• Inborn genetic diseases (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SGCE 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			2	76	3	81
missense	2	6	242	2		252
nonsense	28	3	3			34
start loss						0
frameshift	55	9				64
inframe indel		1	3			4
splice donor/acceptor (+/-2bp)	14	9	1			24
splice region			21	12	1	34
non coding			6	69	25	100
Total	99	28	257	147	28

Highest pathogenic variant AF is 0.0000132

Variants in SGCE

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

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

Position	Type	Phenotype	Significance	ClinVar
7-94533211-A-C		not specified	Uncertain significance (Dec 20, 2021)
7-94535312-C-G		not specified	Uncertain significance (Aug 12, 2021)
7-94535317-T-C		not specified	Uncertain significance (May 27, 2022)
7-94535508-A-C		not specified	Uncertain significance (Jul 06, 2021)
7-94535510-C-T		not specified	Uncertain significance (May 01, 2024)
7-94537545-G-A		not specified	Uncertain significance (Aug 08, 2022)
7-94537559-C-T		not specified	Uncertain significance (Apr 09, 2024)
7-94537640-C-T		not specified	Uncertain significance (Jan 04, 2022)
7-94537733-C-A		not specified	Uncertain significance (Nov 30, 2022)
7-94537790-A-G		not specified	Uncertain significance (Jul 14, 2021)
7-94537799-A-G		not specified	Uncertain significance (Aug 08, 2023)
7-94537810-C-G		not specified	Uncertain significance (Apr 08, 2024)
7-94537820-A-G		not specified	Uncertain significance (Dec 28, 2022)
7-94537848-T-C		not specified	Uncertain significance (Jan 03, 2024)
7-94537883-A-G		not specified	Uncertain significance (May 04, 2022)
7-94545581-T-A		not specified	Uncertain significance (Jan 18, 2023)
7-94545608-T-C		not specified	Uncertain significance (Apr 08, 2024)
7-94545635-G-A		not specified	Uncertain significance (Nov 12, 2021)
7-94545647-G-C		not specified	Uncertain significance (Sep 25, 2023)
7-94545698-A-G		not specified	Uncertain significance (Aug 08, 2023)
7-94549547-G-T		not specified	Uncertain significance (Dec 03, 2021)
7-94551339-T-C		not specified	Uncertain significance (Nov 29, 2023)
7-94551362-G-A		not specified	Uncertain significance (May 20, 2024)
7-94551390-G-A		not specified	Uncertain significance (Oct 16, 2023)
7-94551471-C-T		not specified	Uncertain significance (May 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SGCE	protein_coding	protein_coding	ENST00000445866	12	70980

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0238	0.976	125707	0	23	125730	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.05	207	254	0.814	0.0000133	3014
Missense in Polyphen		64	96.282	0.66472		1165
Synonymous	0.0982	89	90.2	0.987	0.00000480	873
Loss of Function	3.38	8	26.9	0.297	0.00000154	302

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000150	0.000149
Middle Eastern	0.00	0.00
South Asian	0.0000980	0.0000980
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of the sarcoglycan complex, a subcomplex of the dystrophin-glycoprotein complex which forms a link between the F-actin cytoskeleton and the extracellular matrix.
• Disease: DISEASE: Dystonia 11, myoclonic (DYT11) [MIM:159900]: A myoclonic dystonia. Dystonia is defined by the presence of sustained involuntary muscle contractions, often leading to abnormal postures. DYT11 is characterized by involuntary lightning jerks and dystonic movements and postures alleviated by alcohol. Inheritance is autosomal dominant. The age of onset, pattern of body involvement, presence of myoclonus and response to alcohol are all variable. {ECO:0000269|PubMed:11528394, ECO:0000269|PubMed:12402271, ECO:0000269|PubMed:15079037, ECO:0000269|PubMed:15258227, ECO:0000269|PubMed:16227522, ECO:0000269|PubMed:17853490, ECO:0000269|PubMed:18175340, ECO:0000269|PubMed:18362280, ECO:0000269|PubMed:19066193, ECO:0000269|PubMed:21796726}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Recessive Scores

• pRec: 0.231

Intolerance Scores

• loftool: 0.0924
• rvis_EVS: -0.54
• rvis_percentile_EVS: 20.54

Haploinsufficiency Scores

• pHI: 0.423
• hipred: Y
• hipred_score: 0.758
• ghis: 0.578

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.558

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sgce
• Phenotype: muscle phenotype; cellular phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: cell-matrix adhesion;muscle organ development
• Cellular component: Golgi apparatus;cytoskeleton;plasma membrane;integral component of plasma membrane;dystrophin-associated glycoprotein complex;sarcoglycan complex;dendrite membrane;sarcolemma