STAG2

stromal antigen 2, the group of Cohesin complex|Armadillo like helical domain containing

Basic information

Region (hg38): X:123960212-124422664

Links

ENSG00000101972

∙ NCBI:10735 ∙ OMIM:300826 ∙ HGNC:11355 ∙ Uniprot:Q8N3U4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

Mullegama-Klein-Martinez syndrome (Strong), mode of inheritance: XL
Mullegama-Klein-Martinez syndrome (Strong), mode of inheritance: XL
Mullegama-Klein-Martinez syndrome (Strong), mode of inheritance: XL
Mullegama-Klein-Martinez syndrome (Definitive), mode of inheritance: XL
Xq25 microduplication syndrome (Limited), mode of inheritance: XL

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Mullegama-Klein-Martinez syndrome (Neurodevelopmental disorder, X-linked, with craniofacial abnormalities); Holoprosencephaly 13, X-linked	XL	Cardiovascular	The conditions can involve congenital cardiac anomalies, and awareness may allow early management	Cardiovascular; Craniofacial; Musculoskeletal; Neurologic	28296084; 29263825; 30158690; 30447054; 30765867; 31334757

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the STAG2 gene.

not_provided (576 variants)
Mullegama-Klein-Martinez_syndrome (40 variants)
Inborn_genetic_diseases (39 variants)
STAG2-related_disorder (27 variants)
Holoprosencephaly_13,_X-linked (15 variants)
not_specified (5 variants)
Neurodevelopmental_disorder (1 variants)
Intellectual_disability (1 variants)
See_cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the STAG2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001042750.2. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			6 clinvar	112 clinvar	18 clinvar	136
missense	2 clinvar	8 clinvar	250 clinvar	13 clinvar	7 clinvar	280
nonsense	6 clinvar	3 clinvar	2 clinvar			11
start loss						0
frameshift	9 clinvar	2 clinvar	1 clinvar			12
splice donor/acceptor (+/-2bp)	4 clinvar	3 clinvar	4 clinvar	2 clinvar	1 clinvar	14
Total	21	16	263	127	26

Highest pathogenic variant AF is 9.12679e-7

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
STAG2	protein_coding	protein_coding	ENST00000218089	33	462453

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	2.42e-8	121668	0	1	121669	0.00000411

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.94	151	444	0.340	0.0000324	8460
Missense in Polyphen		20	132.2	0.15128		2573
Synonymous	-0.369	146	140	1.04	0.00000971	2208
Loss of Function	6.61	1	52.8	0.0189	0.00000432	926

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000629	0.0000467
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Component of cohesin complex, a complex required for the cohesion of sister chromatids after DNA replication. The cohesin complex apparently forms a large proteinaceous ring within which sister chromatids can be trapped. At anaphase, the complex is cleaved and dissociates from chromatin, allowing sister chromatids to segregate. The cohesin complex may also play a role in spindle pole assembly during mitosis. {ECO:0000269|PubMed:12034751}.;
Pathway: Cell cycle - Homo sapiens (human);Signal Transduction;SUMOylation of DNA damage response and repair proteins;Post-translational protein modification;SUMO E3 ligases SUMOylate target proteins;Metabolism of proteins;Reproduction;SUMOylation;Establishment of Sister Chromatid Cohesion;S Phase;Meiotic synapsis;Meiosis;Signaling by Nuclear Receptors;Mitotic Prometaphase;Separation of Sister Chromatids;Mitotic Anaphase;Mitotic Metaphase and Anaphase;Cohesin Loading onto Chromatin;Mitotic Telophase/Cytokinesis;M Phase;Estrogen-dependent gene expression;Cell Cycle;Resolution of Sister Chromatid Cohesion;Cell Cycle, Mitotic;ESR-mediated signaling;PLK1 signaling events (Consensus)

Intolerance Scores

loftool
rvis_EVS: -0.63
rvis_percentile_EVS: 17.03

Haploinsufficiency Scores

pHI: 0.703
hipred: Y
hipred_score: 0.859
ghis: 0.651

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: H
gene_indispensability_pred: E
gene_indispensability_score: 0.894

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Stag2
Phenotype

Gene ontology

Biological process: sister chromatid cohesion;negative regulation of DNA endoreduplication;cell division;meiotic cell cycle;regulation of mitotic spindle assembly
Cellular component: chromosome, centromeric region;chromatin;nucleus;nucleoplasm;chromosome;cytosol;cohesin complex;membrane;nuclear matrix;mitotic spindle pole
Molecular function: chromatin binding;protein binding