SGCD sarcoglycan delta [Homo sapiens (human)] - Gene

Summary

Official Symbol: SGCDprovided by HGNC
Official Full Name: sarcoglycan deltaprovided by HGNC
Primary source: HGNC:HGNC:10807
See related: Ensembl:ENSG00000170624 MIM:601411; AllianceGenome:HGNC:10807
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: SGD; DAGD; 35DAG; CMD1L; SGCDP; LGMDR6; SG-delta
Summary: The protein encoded by this gene is one of the four known components of the sarcoglycan complex, which is a subcomplex of the dystrophin-glycoprotein complex (DGC). DGC forms a link between the F-actin cytoskeleton and the extracellular matrix. This protein is expressed most abundantly in skeletal and cardiac muscle. Mutations in this gene have been associated with autosomal recessive limb-girdle muscular dystrophy and dilated cardiomyopathy. Alternatively spliced transcript variants encoding distinct isoforms have been observed for this gene. [provided by RefSeq, Jul 2008]
Expression: Broad expression in heart (RPKM 13.1), thyroid (RPKM 9.5) and 17 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 5q33.2-q33.3

Exon count:: 14

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	5	NC_000005.10 (155727832..156767788)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	5	NC_060929.1 (156261684..157286763)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	5	NC_000005.9 (155754174..156194799)

Chromosome 5 - NC_000005.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Study identified 2 non-synonymous missense mutations: c.C652T, p.R218W in ACVRL1, c.C717G, p.D239E in SGCD in Chinese population with total anomalous pulmonary venous return.
Title: Whole-exome sequencing identifies SGCD and ACVRL1 mutations associated with total anomalous pulmonary venous return (TAPVR) in Chinese population.
Dilated cardiomyopathy mutations in delta-sarcoglycan can exert a dominant negative effect on dystrophin-glycoprotein complex function leading to myocardial mechanical instability that may underlie the pathogenesis of delta-sarcoglycan-associated DCM.
Title: Dilated cardiomyopathy mutations in δ-sarcoglycan exert a dominant-negative effect on cardiac myocyte mechanical stability.
haplotype -_G composed of c.-100~-110 and A848G confers higher susceptibility to dilated cardiomyopathy in the Mongoloid population.
Title: A Haplotype of Two Novel Polymorphisms in δ-Sarcoglycan Gene Increases Risk of Dilated Cardiomyopathy in Mongoloid Population.
CC genotype of the delta-sarcoglycan gene polymorphism rs13170573 is associated with obstructive sleep apnea in the Chinese population
Title: The CC genotype of the delta-sarcoglycan gene polymorphism rs13170573 is associated with obstructive sleep apnea in the Chinese population.
Genetic variation at the delta-sarcoglycan locus elevates heritable sympathetic nerve activity in human twin pairs
Title: Genetic variation at the delta-sarcoglycan (SGCD) locus elevates heritable sympathetic nerve activity in human twin pairs.
Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
Observational study of genetic testing. (HuGE Navigator)
Title: A novel custom resequencing array for dilated cardiomyopathy.
Observational study of genotype prevalence. (HuGE Navigator)
Title: Delta-sarcoglycan gene polymorphism frequency in Amerindian and Mestizo populations of Mexico.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
Observational study and genome-wide association study of gene-disease association and gene-gene interaction. (HuGE Navigator)
Title: Detecting Genes and Gene-gene Interactions for Age-related Macular Degeneration with a Forest-based Approach.

Submit: New GeneRIF Correction See all GeneRIFs (16)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Autosomal recessive limb-girdle muscular dystrophy type 2F MedGen: C1832525 OMIM: 601287 GeneReviews: Not available	Compare labs
Dilated cardiomyopathy 1L MedGen: C1847667 OMIM: 606685 GeneReviews: Not available	Compare labs
Limb-girdle muscular dystrophy MedGen: C0686353 GeneReviews: Not available	Compare labs
Primary dilated cardiomyopathy MedGen: C0007193 GeneReviews: Dilated Cardiomyopathy Overview	Compare labs

EBI GWAS Catalog

Description
Gene network analysis in a pediatric cohort identifies novel lung function genes. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association study of anthropometric traits in Korcula Island, Croatia. EBI GWAS Catalog EBI GWAS CatalogPubMed
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH103477 (e-PCR)
- UniSTS:97802

RH119027 (e-PCR)
- UniSTS:138256

NIB2057 (e-PCR)
- UniSTS:531

G64134 (e-PCR)
- UniSTS:146743

SHGC-153999 (e-PCR)
- UniSTS:184125

SHGC-142716 (e-PCR)
- UniSTS:171609

SHGC-79724 (e-PCR)
- UniSTS:101227

RH41990 (e-PCR)
- UniSTS:29558

G64955 (e-PCR)
- UniSTS:164986

D5S1499 (e-PCR)
- UniSTS:38528

RH36417 (e-PCR)
- UniSTS:70274

SHGC-83016 (e-PCR)
- UniSTS:96130

RH122565 (e-PCR)
- UniSTS:138629

D5S820 (e-PCR), detects polymorphism
- UniSTS:21140

RH80699 (e-PCR)
- UniSTS:84631

SHGC-14004 (e-PCR)
- UniSTS:63383

bac5714T (e-PCR)
- UniSTS:181662

SGCD__5392 (e-PCR)
- UniSTS:464543

bac5715T (e-PCR)
- UniSTS:181663

WI-14133 (e-PCR)
- UniSTS:34476

A006N34 (e-PCR)
- UniSTS:60634

STS-U58331 (e-PCR)
- UniSTS:39142

SHGC-81762 (e-PCR)
- UniSTS:103923

L31456 (e-PCR)
- UniSTS:18430

Gene Ontology Provided by GOA

Process	Evidence Code	Pubs
involved_in calcium ion homeostasis	IEA Inferred from Electronic Annotation more info
involved_in calcium-mediated signaling	IEA Inferred from Electronic Annotation more info
involved_in cardiac muscle cell contraction	IEA Inferred from Electronic Annotation more info
involved_in cardiac muscle cell development	IEA Inferred from Electronic Annotation more info
involved_in cardiac muscle tissue development	IBA Inferred from Biological aspect of Ancestor more info
involved_in coronary vasculature morphogenesis	IEA Inferred from Electronic Annotation more info
involved_in heart contraction	IBA Inferred from Biological aspect of Ancestor more info
involved_in muscle organ development	TAS Traceable Author Statement more info	PubMed
involved_in protein-containing complex localization	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cytoskeleton	IEA Inferred from Electronic Annotation more info
part_of dystrophin-associated glycoprotein complex	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	TAS Traceable Author Statement more info	PubMed
part_of sarcoglycan complex	IBA Inferred from Biological aspect of Ancestor more info
is_active_in sarcolemma	IBA Inferred from Biological aspect of Ancestor more info
located_in sarcoplasmic reticulum	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: delta-sarcoglycan

Names: 35 kDa dystrophin-associated glycoprotein; delta-SG; dystrophin associated glycoprotein, delta sarcoglycan; placental delta sarcoglycan; sarcoglycan, delta (35kDa dystrophin-associated glycoprotein)

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_008693.2 RefSeqGene

Range

461414..902446

Download

GenBank, FASTA, Sequence Viewer (Graphics), LRG_205

mRNA and Protein(s)

NM_000337.6 → NP_000328.2 delta-sarcoglycan isoform 1

See identical proteins and their annotated locations for NP_000328.2

Status: REVIEWED

Description

Transcript Variant: This variant (1, also known as SGCD1), encodes the longest isoform (1).

Source sequence(s)

AC025434, BC020740, BQ434817, BQ446019, BX537948

Consensus CDS

CCDS47325.1

UniProtKB/Swiss-Prot

Q92629

Related

ENSP00000338343.4, ENST00000337851.9

Conserved Domains (1) summary

pfam04790
Location:24 → 278

Sarcoglycan_1; Sarcoglycan complex subunit protein
NM_001128209.2 → NP_001121681.1 delta-sarcoglycan isoform 3

See identical proteins and their annotated locations for NP_001121681.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) is lacking an internal exon from the 5' end compared to transcript variant 1, resulting in translation initiation from the second in-frame AUG, and an isoform (3) missing 1 aa at the N-terminus compared to isoform 1.

Source sequence(s)

AC025434, BC020740, BQ434817, BQ446019, BX537948, DA561069

Consensus CDS

CCDS47327.1

UniProtKB/Swiss-Prot

A8K9S9, Q53XA5, Q92629, Q99644

Related

ENSP00000403003.2, ENST00000435422.7

Conserved Domains (1) summary

pfam04790
Location:23 → 277

Sarcoglycan_1; Sarcoglycan complex subunit protein
NM_172244.3 → NP_758447.1 delta-sarcoglycan isoform 2

See identical proteins and their annotated locations for NP_758447.1

Status: REVIEWED

Description

Transcript Variant: This variant (2, also known as SGCD2), contains an alternate 3' terminal exon compared to transcript variant 1. This results in a shorter isoform (2) with a distinct C-terminus compared to isoform 1.

Source sequence(s)

AI139498, BQ434817, U58331

Consensus CDS

CCDS47326.1

UniProtKB/Swiss-Prot

Q92629

Related

ENSP00000429378.1, ENST00000517913.5

Conserved Domains (1) summary

pfam04790
Location:29 → 235

Sarcoglycan_1; Sarcoglycan complex subunit protein

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000005.10 Reference GRCh38.p14 Primary Assembly

Range

155727832..156767788

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047417519.1 → XP_047273475.1 delta-sarcoglycan isoform X1
XM_047417518.1 → XP_047273474.1 delta-sarcoglycan isoform X1
XM_017009724.2 → XP_016865213.1 delta-sarcoglycan isoform X1

UniProtKB/Swiss-Prot

Q92629

Conserved Domains (1) summary

pfam04790
Location:24 → 278

Sarcoglycan_1; Sarcoglycan complex subunit protein
XM_047417520.1 → XP_047273476.1 delta-sarcoglycan isoform X2

UniProtKB/Swiss-Prot

A8K9S9, Q53XA5, Q92629, Q99644
XM_005265967.3 → XP_005266024.1 delta-sarcoglycan isoform X3

Conserved Domains (1) summary

pfam04790
Location:29 → 166

Sarcoglycan_1; Sarcoglycan complex subunit protein
XM_005265966.6 → XP_005266023.1 delta-sarcoglycan isoform X1

See identical proteins and their annotated locations for XP_005266023.1

UniProtKB/Swiss-Prot

Q92629

Conserved Domains (1) summary

pfam04790
Location:24 → 278

Sarcoglycan_1; Sarcoglycan complex subunit protein