SGO1

shugoshin 1

Basic information

Region (hg38): 3:20160592-20186206

Previous symbols: [ "SGOL1" ]

Links

ENSG00000129810 ∙ NCBI:151648 ∙ OMIM:609168 ∙ HGNC:25088 ∙ Uniprot:Q5FBB7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• chronic atrial and intestinal dysrhythmia (Supportive), mode of inheritance: AR
• chronic atrial and intestinal dysrhythmia (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Chronic atrial and intestinal dysrhythmia	AD	Cardiovascular; Gastrointestinal	The condition can involve arrthymias and valve anomalies, and awareness may allow early diagnosis and management (eg, with pacemakers); Individuals have been described with intestinal pseudoobstruction, and nutritional support, such as with TPN, has been described	Cardiovascular; Gastrointestinal	25282101

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SGO1 gene.

• not provided (6 variants)
• Chronic atrial and intestinal dysrhythmia (2 variants)
• Inborn genetic diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SGO1 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	2
missense	1		2	1	2	6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	1	0	2	1	4

Highest pathogenic variant AF is 0.000138

Variants in SGO1

This is a list of pathogenic ClinVar variants found in the SGO1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-20174353-G-C		Chronic atrial and intestinal dysrhythmia	Uncertain significance (Dec 06, 2021)
3-20174380-G-A		SGO1-related disorder	Likely benign (Mar 21, 2022)
3-20174566-T-G		SGO1-related disorder	Benign (Dec 31, 2019)
3-20174605-T-C			Likely benign (Jul 13, 2018)
3-20174877-C-T			Benign (Dec 31, 2019)
3-20174992-G-A		not specified	Uncertain significance (Jun 11, 2021)
3-20175019-A-G			Benign (Dec 31, 2019)
3-20175027-T-A		SGO1-related disorder	Benign (Oct 17, 2019)
3-20183961-T-C		Chronic atrial and intestinal dysrhythmia	Pathogenic (Jan 11, 2023)
3-20183998-G-T		SGO1-related disorder	Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SGO1	protein_coding	protein_coding	ENST00000263753	8	25700

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.59e-12	0.137	125690	0	35	125725	0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.577	305	278	1.10	0.0000137	3697
Missense in Polyphen		57	57.246	0.99571		811
Synonymous	-0.380	104	99.2	1.05	0.00000506	1013
Loss of Function	0.707	20	23.7	0.843	0.00000135	320

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000129	0.000120
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000290	0.000272
Finnish	0.000140	0.000139
European (Non-Finnish)	0.000127	0.000123
Middle Eastern	0.000290	0.000272
South Asian	0.000313	0.000294
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a central role in chromosome cohesion during mitosis by preventing premature dissociation of cohesin complex from centromeres after prophase, when most of cohesin complex dissociates from chromosomes arms. May act by preventing phosphorylation of the STAG2 subunit of cohesin complex at the centromere, ensuring cohesin persistence at centromere until cohesin cleavage by ESPL1/separase at anaphase. Essential for proper chromosome segregation during mitosis and this function requires interaction with PPP2R1A. Its phosphorylated form is necessary for chromosome congression and for the proper attachment of spindle microtubule to the kinetochore. Necessary for kinetochore localization of PLK1 and CENPF. May play a role in the tension sensing mechanism of the spindle-assembly checkpoint by regulating PLK1 kinetochore affinity. Isoform 3 plays a role in maintaining centriole cohesion involved in controlling spindle pole integrity. Involved in centromeric enrichment of AUKRB in prometaphase. {ECO:0000269|PubMed:15604152, ECO:0000269|PubMed:15723797, ECO:0000269|PubMed:15737064, ECO:0000269|PubMed:16580887, ECO:0000269|PubMed:17617734, ECO:0000269|PubMed:17621308, ECO:0000269|PubMed:18331714, ECO:0000269|PubMed:20739936}.
• Disease: DISEASE: Chronic atrial and intestinal dysrhythmia (CAID) [MIM:616201]: A disease characterized by dysregulation of the cardiac sinus node resulting in sick sinus syndrome, in association with chronic intestinal pseudo-obstruction, a disorder of gastrointestinal motility in which intestinal obstruction occurs in the absence of a mechanical obstacle. {ECO:0000269|PubMed:25282101}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Oocyte meiosis - Homo sapiens (human);Signal Transduction;Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal;Amplification of signal from the kinetochores;Mitotic Spindle Checkpoint;Cell Cycle Checkpoints;RHO GTPases Activate Formins;RHO GTPase Effectors;Signaling by Rho GTPases;Mitotic Prometaphase;Separation of Sister Chromatids;Mitotic Anaphase;Mitotic Metaphase and Anaphase;M Phase;Cell Cycle;Resolution of Sister Chromatid Cohesion;Cell Cycle, Mitotic;Aurora B signaling;PLK1 signaling events (Consensus)

Recessive Scores

• pRec: 0.0775

Intolerance Scores

• rvis_EVS: 0.71
• rvis_percentile_EVS: 85.68

Haploinsufficiency Scores

• pHI: 0.0675
• hipred: Y
• hipred_score: 0.518

Essentials

• essential_gene_gene_trap: E

Mouse Genome Informatics

• Gene name: Sgo1
• Phenotype: digestive/alimentary phenotype; neoplasm; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cellular phenotype; homeostasis/metabolism phenotype; endocrine/exocrine gland phenotype

Zebrafish Information Network

• Gene name: sgo1
• Affected structure: pericardium
• Phenotype tag: abnormal
• Phenotype quality: edematous

Gene ontology

• Biological process: chromosome segregation;attachment of spindle microtubules to kinetochore;centriole-centriole cohesion;meiotic chromosome segregation;cell division;mitotic sister chromatid cohesion, centromeric
• Cellular component: chromosome, centromeric region;kinetochore;condensed chromosome kinetochore;condensed chromosome, centromeric region;spindle pole;nucleoplasm;centrosome;cytosol
• Molecular function: protein binding;kinase binding