SGCA (sarcoglycan alpha)

Gene

• Entrez ID: 6442
• Gene name: Sarcoglycan alpha
• Gene symbol: SGCA
• Synonyms (NCBI Gene): 50DAG, ADL, DAG2, DMDA2, LGMD2D, LGMDR3, SCARMD1, adhalin
• Chromosome: 17
• Chromosome location: 17q21.33
• Summary: This gene encodes a component of the dystrophin-glycoprotein complex (DGC), which is critical to the stability of muscle fiber membranes and to the linking of the actin cytoskeleton to the extracellular matrix. Its expression is thought to be restricted t

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs35972733	G>A,T	Conflicting-interpretations-of-pathogenicity, likely-benign	Synonymous variant, intron variant, non coding transcript variant, coding sequence variant
rs137852623	C>G,T	Pathogenic, pathogenic-likely-pathogenic	Coding sequence variant, intron variant, non coding transcript variant, missense variant
rs138019537	C>T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, intron variant, non coding transcript variant, missense variant
rs139454982	G>A,C	Conflicting-interpretations-of-pathogenicity, likely-benign, uncertain-significance	Coding sequence variant, intron variant, synonymous variant, non coding transcript variant
rs143570936	G>A	Pathogenic, pathogenic-likely-pathogenic	Coding sequence variant, intron variant, non coding transcript variant, missense variant
rs149487996	C>A	Conflicting-interpretations-of-pathogenicity	Intron variant, synonymous variant, non coding transcript variant, coding sequence variant
rs200166783	G>A,T	Uncertain-significance, pathogenic-likely-pathogenic	Intron variant, missense variant, non coding transcript variant, coding sequence variant
rs368522117	C>T	Conflicting-interpretations-of-pathogenicity	Non coding transcript variant, synonymous variant, stop gained, coding sequence variant
rs369385261	G>A	Conflicting-interpretations-of-pathogenicity	Intron variant
rs757481230	C>A,T	Likely-pathogenic, uncertain-significance	Coding sequence variant, missense variant, intron variant, non coding transcript variant
rs763372958	G>A,T	Likely-pathogenic	Coding sequence variant, stop gained, missense variant, non coding transcript variant
rs796065318	->CG	Likely-pathogenic	Frameshift variant, coding sequence variant, non coding transcript variant
rs886043392	G>A	Pathogenic	Intron variant, splice donor variant
rs886043962	C>-	Pathogenic	Frameshift variant, coding sequence variant, intron variant, non coding transcript variant
rs886044512	C>-	Pathogenic	Frameshift variant, coding sequence variant, intron variant, non coding transcript variant
rs1057516548	A>-	Likely-pathogenic	Frameshift variant, coding sequence variant, non coding transcript variant, intron variant
rs1057516729	AG>T	Likely-pathogenic	Frameshift variant, coding sequence variant, non coding transcript variant, intron variant
rs1057517377	AA>-	Likely-pathogenic	Frameshift variant, coding sequence variant, non coding transcript variant, intron variant
rs1220674950	G>-	Likely-pathogenic	Splice acceptor variant, intron variant, coding sequence variant, non coding transcript variant
rs1342189589	G>A,C	Pathogenic	Intron variant, splice acceptor variant
rs1412537279	A>T	Likely-pathogenic	Splice acceptor variant, intron variant, non coding transcript variant
rs1555568965	A>C,T	Likely-pathogenic	Intron variant, splice acceptor variant
rs1555569339	G>T	Likely-pathogenic	Intron variant, stop gained, non coding transcript variant, coding sequence variant
rs1555569342	TGAATGTGGGCATGAAGG>-	Likely-pathogenic	Splice donor variant, intron variant, non coding transcript variant, coding sequence variant
rs1567741398	C>T	Pathogenic	Intron variant, stop gained, non coding transcript variant, coding sequence variant
rs1598277713	->ATGG	Pathogenic	Frameshift variant, coding sequence variant, non coding transcript variant

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000139	Component	Golgi membrane	TAS
GO:0005509	Function	Calcium ion binding	IEA
GO:0005515	Function	Protein binding	IPI	21516116, 25416956, 25910212, 26871637, 32296183, 32814053
GO:0005737	Component	Cytoplasm	IEA
GO:0005789	Component	Endoplasmic reticulum membrane	TAS
GO:0005856	Component	Cytoskeleton	IEA
GO:0005886	Component	Plasma membrane	IEA
GO:0005886	Component	Plasma membrane	TAS
GO:0005911	Component	Cell-cell junction	IEA
GO:0006936	Process	Muscle contraction	TAS	8069911
GO:0007517	Process	Muscle organ development	TAS	7663524
GO:0016010	Component	Dystrophin-associated glycoprotein complex	IEA
GO:0016010	Component	Dystrophin-associated glycoprotein complex	TAS	7937874
GO:0016011	Component	Dystroglycan complex	IEA
GO:0016012	Component	Sarcoglycan complex	IBA
GO:0016012	Component	Sarcoglycan complex	IEA
GO:0016020	Component	Membrane	IEA
GO:0042383	Component	Sarcolemma	IEA
GO:0045121	Component	Membrane raft	IEA

Other IDs

• MIM: 600119
• HGNC: 10805
• e!Ensembl: ENSG00000108823

Protein

• UniProt ID: Q16586
• Protein name: Alpha-sarcoglycan (Alpha-SG) (50 kDa dystrophin-associated glycoprotein) (50DAG) (Adhalin) (Dystroglycan-2)
• Protein 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.
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF05510	Sarcoglycan_2	7 → 382	Sarcoglycan alpha/epsilon	Family

• Tissue specificity: TISSUE SPECIFICITY: Most strongly expressed in skeletal muscle. Also expressed in cardiac muscle and, at much lower levels, in lung. In the fetus, most abundant in cardiac muscle and, at lower levels, in lung. Also detected in liver and kidney. Not expres
• Sequence:

  MAETLFWTPLLVVLLAGLGDTEAQQTTLHPLVGRVFVHTLDHETFLSLPEHVAVPPAVHI
  TYHAHLQGHPDLPRWLRYTQRSPHHPGFLYGSATPEDRGLQVIEVTAYNRDSFDTTRQRL
  VLEIGDPEGPLLPYQAEFLVRSHDAEEVLPSTPASRFLSALGGLWEPGELQLLNVTSALD
  RGGRVPLPIEGRKEGVYIKVGSASPFSTCLKMVASPDSHARCAQGQPPLLSCYDTLAPHF
  RVDWCNVTLVDKSVPEPADEVPTPGDGILEHDPFFCPPTEAPDRDFLVDALVTLLVPLLV
  ALLLTLLLAYVMCCRREGRLKRDLATSDIQMVHHCTIHGNTEELRQMAASREVPRPLSTL
  PMFNVHTGERLPPRVDSAQVPLILDQH

• Sequence length: 387

Pathways

KEGG:

Cytoskeleton in muscle cells
Hypertrophic cardiomyopathy
Arrhythmogenic right ventricular cardiomyopathy
Dilated cardiomyopathy
Viral myocarditis

Associated diseases

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Abnormality of the musculature	Likely pathogenic; Pathogenic	rs2144493345, rs2144494074, rs2144495228, rs28933693, rs387907298	RCV001814459 RCV001814397 RCV001814458 RCV001813971 RCV001836716
Autosomal recessive limb-girdle muscular dystrophy	Likely pathogenic; Pathogenic	rs2509113878, rs143570936, rs757888349, rs890921874, rs760608643, rs758647756, rs1373671710, rs2509117903, rs137852621, rs28933693, rs137852623, rs886041387, rs138945081, rs780264754, rs757481230, rs748936034, rs387907298, rs138254713, rs1342189589, rs1904986620, rs1391089933, rs371675217, rs398123098	RCV002281872 RCV002271422 RCV003330528 RCV005433332 RCV004998385 RCV004998420 RCV003123566 RCV003155829 RCV002307361 RCV003987316 RCV001194149 RCV003114441 RCV004701375 RCV006445648 RCV003317182 RCV005000097 RCV004998112 RCV005000367 RCV005000368 RCV004689979 RCV004998780 RCV004998203 RCV004998204
Autosomal recessive limb-girdle muscular dystrophy type 2D	Pathogenic; Likely pathogenic	rs2144494148, rs2144498403, rs111386656, rs2144502043, rs2144493135, rs1905070544, rs780264754, rs2144495228, rs2144493097, rs2144501172, rs76542495, rs2144498121, rs2144496721, rs2144498569, rs2144500924, rs398123098, rs2144494642, rs758647756, rs2144493427, rs779439298, rs1473539605, rs2144494297, rs2144498132, rs2144493323, rs1017592342, rs2144501024, rs2144497138, rs2509123275, rs2509125625, rs2509113878, rs143570936, rs759624003, rs2509118076, rs2509117896, rs757888349, rs768814872, rs765864199, rs796065318, rs890921874, rs760608643, rs763986788, rs1482631076, rs2509118949, rs2509118810, rs2509119198, rs1342319346, rs1373671710, rs137852621, rs137852622, rs28933693, rs397514451, rs137852623, rs886041387, rs138945081, rs886043221, rs372210292, rs886043392, rs886043962, rs757481230, rs753650776, rs766400853, rs886044688, rs201860673, rs2509123048, rs2509122225, rs2509121499, rs2509121804, rs2509117878, rs2509125245, rs1384158714, rs1370709181, rs2509133581, rs2509118207, rs2509119030, rs2509113935, rs1228963839, rs2509125153, rs2509133663, rs2509118693, rs2509122255, rs1057516888, rs370819630, rs145697858, rs2509113948, rs1567741236, rs2509118765, rs1352135631, rs1598266203, rs749205073, rs1184946403, rs1057517107, rs1057516300, rs1057516650, rs1057517142, rs1057516242, rs1057516664, rs1057517377, rs1057516548, rs1057516729, rs144356125, rs1555568335, rs1555568318, rs748936034, rs387907298, rs752640127, rs200166783, rs1327595249, rs1555568518, rs1555568264, rs138254713, rs1342189589, rs112500642, rs1220674950, rs1412537279, rs1555568775, rs1555569339, rs903823830, rs1555568965, rs1555569342, rs763372958, rs1555568325, rs1555568396, rs1161291343, rs1555568876, rs1567739339, rs1567739228, rs1598277713, rs1567739735, rs1567741398, rs1387802849, rs1598265248, rs1904771410, rs1904986620, rs1905103030, rs1905167458, rs1905254738, rs1905256830, rs760989961, rs113109898, rs774299871, rs1391089933, rs371675217	RCV001360645 RCV001360119 RCV001377955 RCV001377786 RCV001380121 RCV001386680 RCV001380152 RCV005409822 RCV001582428 RCV001784968 RCV001989364 RCV002013697 RCV002019216 RCV001985841 RCV001941636 RCV001930566 RCV002041840 RCV002019675 RCV001981888 RCV002002976 RCV001893883 RCV001917918 RCV001989171 RCV002002557 RCV001963134 RCV001883739 RCV002003503 RCV002005157 RCV002466746 RCV002466747 RCV003621621 RCV000179241 RCV002309691 RCV002310513 RCV002310519 RCV000169146 RCV000169036 RCV003073926 RCV003474923 RCV002629406 RCV000648057 RCV002642509 RCV002727063 RCV002842269 RCV002880920 RCV002972132 RCV000201165 RCV003020880 RCV003509775 RCV000010042 RCV000010043 RCV000010044 RCV000010045 RCV000010046 RCV003233535 RCV000309945 RCV000286102 RCV000403326 RCV000341255 RCV001378409 RCV003621525 RCV000675091 RCV000411266 RCV003334456 RCV003338032 RCV003133209 RCV003472659 RCV003472660 RCV003472662 RCV003472663 RCV003472664 RCV003472665 RCV003472666 RCV003472667 RCV003472668 RCV003472669 RCV003472670 RCV003472671 RCV003472672 RCV003472673 RCV003472674 RCV003463544 RCV003486338 RCV003486339 RCV003486340 RCV003510670 RCV003509020 RCV003509021 RCV003622754 RCV003623093 RCV003623429 RCV004573573 RCV004573575 RCV004573576 RCV004573577 RCV004573578 RCV000411207 RCV000409677 RCV000410516 RCV000412176 RCV000410508 RCV000410603 RCV000409089 RCV000411377 RCV000409217 RCV000410962 RCV000411428 RCV000536997 RCV001824141 RCV000499843 RCV000669831 RCV000030783 RCV000529542 RCV000553098 RCV000531212 RCV000648060 RCV002530966 RCV003139891 RCV001783095 RCV003471962 RCV000984214 RCV000668485 RCV000671062 RCV000672180 RCV000665054 RCV000665422 RCV000669806 RCV000665388 RCV000670790 RCV000664601 RCV000671951 RCV000665165 RCV000705167 RCV000705659 RCV000706234 RCV000695383 RCV001862188 RCV003472264 RCV003621568 RCV001381638 RCV000786065 RCV000792267 RCV000855431 RCV001046661 RCV001067642 RCV001063795 RCV001038073 RCV001051164 RCV001057349 RCV001062845 RCV001050871 RCV001221207 RCV001255990 RCV000169164 RCV001854369
Limb-girdle muscular dystrophy	Pathogenic	rs28933693	RCV005624683
Muscular dystrophy	Likely pathogenic; Pathogenic	rs138945081	RCV004798826
Sarcoglycanopathy	Likely pathogenic; Pathogenic	rs143570936, rs28933693, rs137852623	RCV000779226 RCV000779225 RCV000778108
See cases	Likely pathogenic; Pathogenic	rs143570936	RCV002252007
SGCA-related disorder	Likely pathogenic; Pathogenic	rs757481230, rs398123098	RCV004755847 RCV004755760

Unknown
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Arrhythmogenic right ventricular cardiomyopathy	Conflicting classifications of pathogenicity	rs759284746	RCV000852721
Cardiomyopathy	Benign; Conflicting classifications of pathogenicity	rs35495899, rs35130237	RCV000852724 RCV000852723
Dystrophin deficiency	Benign	rs1801191, rs149296410	RCV001272917 RCV001271889
Elevated circulating creatine kinase concentration	Likely benign	rs755825098	RCV003228091
Hypertrophic cardiomyopathy	Conflicting classifications of pathogenicity	rs200137051	RCV000852722
Proximal muscle weakness	Uncertain significance	rs558473298	RCV002226558
Qualitative or quantitative defects of alpha-sarcoglycan	Conflicting classifications of pathogenicity	rs1555569329	RCV002531293

Associations from Text Mining
Disease Name	Relationship Type	References
Bundle Branch Block	Associate	33567613
Cardiomyopathies	Associate	10662809
Cardiomyopathy Dilated	Associate	9505924
Cardiomyopathy Right Ventricular Dilated	Associate	33567613
Charcot Marie Tooth disease Type 2F	Associate	24565866
Developmental Disabilities	Associate	37628638
Glycogen Storage Disease Type II	Associate	31931849
Heart Diseases	Associate	10662809
Limb girdle muscular dystrophy autosomal recessive	Associate	11303236
Limb girdle muscular dystrophy type 2B	Associate	26916285, 37628638
Limb girdle muscular dystrophy type 2C	Associate	33386810, 7657792
Limb girdle muscular dystrophy type 2C	Inhibit	7657792
Lymphedema Congenital Recessive	Associate	31931849
Multiple Sclerosis	Associate	36680379
Muscle Weakness	Associate	37628638
Muscular Diseases	Associate	35239206
Muscular Dystrophies	Associate	16258658, 19835634, 37628638, 7657792, 8040315, 9192266, 9393893
Muscular Dystrophies Limb Girdle	Associate	16787395, 24565866, 26934379, 27708273, 32576226, 35239206, 8943294
Muscular Dystrophy Duchenne	Associate	7657792
Muscular Dystrophy Limb Girdle Type 1E	Associate	32576226
Myalgia	Associate	33458577
Nephrosis Lipoid	Associate	7657792
Neuromuscular Diseases	Associate	33567613
Sarcoglycanopathies	Associate	18535179, 19798725, 21031578, 24565866, 29351619, 30764848, 30989758, 31061434, 33386810, 33458577, 9192266, 9475163
Sarcoglycanopathies	Stimulate	39755676
Sarcoglycanopathies	Inhibit	9429136