SGCZ

sarcoglycan zeta, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 8:14084844-15238431

Links

ENSG00000185053 ∙ NCBI:137868 ∙ OMIM:608113 ∙ HGNC:14075 ∙ Uniprot:Q96LD1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

• Inborn genetic diseases (19 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SGCZ 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						0
missense			17	2		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	2	0

Variants in SGCZ

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

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

Position	Type	Phenotype	Significance	ClinVar
8-14090486-C-T		not specified	Uncertain significance (Feb 10, 2023)
8-14090511-G-A		not specified	Uncertain significance (Sep 26, 2023)
8-14090573-G-A		not specified	Uncertain significance (Dec 28, 2022)
8-14090583-A-G		not specified	Uncertain significance (Aug 16, 2021)
8-14090612-T-C		not specified	Likely benign (Jan 09, 2023)
8-14090634-A-G		not specified	Uncertain significance (Dec 13, 2022)
8-14102397-A-C		not specified	Uncertain significance (Apr 06, 2022)
8-14102408-T-C		not specified	Uncertain significance (Jan 17, 2024)
8-14102421-C-G		not specified	Uncertain significance (Dec 16, 2022)
8-14108170-C-A		not specified	Uncertain significance (Jun 23, 2021)
8-14108196-G-A		not specified	Uncertain significance (Nov 08, 2022)
8-14108224-C-T		not specified	Uncertain significance (May 23, 2023)
8-14164625-C-A		not specified	Uncertain significance (Oct 17, 2023)
8-14237595-T-C		not specified	Likely benign (Jan 26, 2023)
8-14324196-C-T		not specified	Uncertain significance (Feb 03, 2022)
8-14554752-T-G		not specified	Uncertain significance (Dec 14, 2022)
8-14554764-T-C		not specified	Uncertain significance (Apr 11, 2023)
8-14554790-G-T		not specified	Uncertain significance (Sep 26, 2022)
8-14554794-C-T		not specified	Uncertain significance (Sep 14, 2022)
8-14554795-C-A		not specified	Uncertain significance (Jul 14, 2023)
8-14554819-T-G		not specified	Uncertain significance (Aug 14, 2023)
8-14554835-C-A		not specified	Uncertain significance (Nov 18, 2022)
8-14554898-G-A		not specified	Uncertain significance (Sep 14, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SGCZ	protein_coding	protein_coding	ENST00000382080	8	1148476

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.40e-9	0.434	125720	0	28	125748	0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.02	201	164	1.22	0.00000803	1994
Missense in Polyphen		61	52.758	1.1562		674
Synonymous	-3.86	102	63.0	1.62	0.00000322	628
Loss of Function	0.940	15	19.5	0.770	0.00000123	199

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000366	0.000334
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.0000467	0.0000462
European (Non-Finnish)	0.000170	0.000167
Middle Eastern	0.0000545	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

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. May play a role in the maintenance of striated muscle membrane stability (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.239
• rvis_EVS: -0.43
• rvis_percentile_EVS: 25.37

Haploinsufficiency Scores

• pHI: 0.478
• hipred: Y
• hipred_score: 0.502
• ghis: 0.423

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sgcz

Gene ontology

• Biological process: muscle cell cellular homeostasis;cardiac muscle tissue development;muscle cell development;heart contraction;membrane organization
• Cellular component: cytoplasm;cytoskeleton;sarcoglycan complex;integral component of membrane;sarcolemma