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Intellectual disability

Gene: STAG2

Green List (high evidence)
STAG2 (stromal antigen 2)
EnsemblGeneIds (GRCh38): ENSG00000101972
EnsemblGeneIds (GRCh37): ENSG00000101972
OMIM: 300826, Gene2Phenotype
STAG2 is in 6 panels

2 reviews

Rebecca Foulger (Genomics England curator)

Comment on list classification: Updated rating from Grey to Green. STAG2 gene added to panel and reviewed Green by Konstantinos Varvagiannis. Confirmed DD-G2P rating for ''STAG2-related developmental delay with microcephaly and congenital anomalies' (note that DD-G2P has monoallelic (not X-linked) inheritance listed). Sufficient cases of STAG2 variants from the literature supporting causation for ID/DD (1 girl from PMID:28296084, 5 males from one family in PMID:29263825, one male in PMID:30447054, plus PMID:30158690).
Created: 26 Feb 2019, 11:24 a.m.
Comment on mode of inheritance: PMID:29263825 report syndromic mental retardation in an X-linked recessive pattern (with two healthy female carriers) wheras PMID:28296084 report an 8 year old girl with a heterozygous variant and ID phenotype. Therefore have selected XLD inheritance in PanelApp to catch all cases.
Created: 26 Feb 2019, 11:22 a.m.
PMID:30447054 (Mullegama et al, 2018) report a 4 year old male with DD, failure to thrive, short stature and polydactyly with a likely pathogenic STAG2 de novo hemizygous variant c.3027A>T, p.Lys1009Asn.
Created: 26 Feb 2019, 11:18 a.m.
PMID:29263825 (Soardi et al., 2017) report 5 individuals from a pedigree with a STAG2 p.Ser327Asn (c.980 G > A) variant that perfectly cosegregates with a phenotype of syndromic mental retardation in a characteristic X-linked recessive pattern- heterozygous female carriers of the variant (aunt and mother of the proband) were healthy. Other healthy relatives did not have the c.980 G>A variant.
Created: 26 Feb 2019, 11:16 a.m.
PMID:28296084 (Mullegama et al, 2017) report an 8 year old girl with global DD, microcephaly, microtia with hearing loss, language delay, ADHD, and dysmorphic features. She had a heterozygous de novo variant in STAG2 (c.205C>T; p.Arg69*). The authors identified 2 additional female cases from the DECIPHER research database with variants in STAG2 (p.Arg604Gln and p.Ala638Valfs*10) and phenotypes similar to their patient- these phenotypes were limited to HPO terms and lack specific clinical details- ID is not listed specifically for these additional cases (Table 1).
Created: 26 Feb 2019, 11:15 a.m.
Created: 26 Feb 2019, 11:15 a.m.

Panel version: 2.766

Konstantinos Varvagiannis (Other)

Green List (high evidence)

Several affected individuals (from at least 8 unrelated) families have been reported in the literature. The phenotype consists - among others - of DD/ID. STAG2 is located on long arm of chromosome X (Xq25). Based on these reports, both males and females can be affected.

Soardi et al. (2017 - PMID: 29263825) report an affected male belonging to a large pedigree with 4 other similarly affected males. The disorder in this pedigree followed a typical X-linked inheritance pattern. All affected males were hemizygous for a missense variant (NM_001042749.1:c.980G>A or p.Ser327Asn). Common phenotype consisted of moderate ID, short stature, sensory hearing loss and some similar facial features. Unaffected males did not harbor the variant. Heterozygous females were not affected. Co-segragation of the variant with the affected status under an X-linked model, appeared unlikely to have occurred by chance (probability of 1/131,072 - logarithm of odds score of 5.12).

Mullegama et al. (2017 - PMID: 28296084) report on an 8-year-old girl harboring a de novo nonsense variant in STAG2 (NM_001042749.1:c.205C>T or p.Arg69Ter). This individual presented - among others with - DD, microcephaly, growth delay, digit anomalies, particular facial features, and anomalies of other systems (eg. hearing loss, cardiac defect, etc). The authors summarize the features of 2 subjects from the DDD study as available in DECIPHER, without additional details. [Variants of these individuals NM_001042749.1:c.1913_1922del10 or p.(A638Vfs*10) / NM_001042749.1:c.1811G>A p.(R604Q)].

Yuan et al. (2018 - PMID: 30158690) report on 4 females with de novo LoF STAG2 variants as well as 1 male subject with a de novo missense one. DD (5/5) and ID (4/4) were features in all individuals for whom this information was available. One additional female had an intragenic STAG2 deletion, although this subject was not reported to have DD or ID (table S6 : microcephaly, seizures and facial phenotype). It is not known whether the deletion was inherited or had occurred as a de novo event. All variants from this study have been submitted in ClinVar (phenotype : STAG2-related disorder).

Mullegama et al. (2018 - PMID: 30447054) report on a 4-year-old male with DD, microcephaly, growth delay, digit anomalies due to a de novo missense STAG2 variant (c.3027A>T or p.Lys1009Asn). As discussed by the authors at the time of the study 33 males with Xq25 duplications and ID had been reported (PMIDs cited: 19449417, 26443594, 25677961, 23637084, 25450604).

Discussed in these articles :

STAG2 (or STAG1) is one of the 4 core proteins of the cohesin complex, the other 3 being SMC1A, SMC3 and RAD21. Mutations in genes encoding these proteins or their interactors (eg. NIBPL, HDAC8, ESCO2, etc) have been associated cohesinopathies, a group of multisystem developmental disorders (eg. Cornelia de Lange syndrome, Roberts/SC phocomelia, etc).

It has been commented that the phenotype of STAG2-related disorder presents overlap with other cohesinopathies (eg. DD, microcephaly and growth retardation, craniofacial features, anomalies of the digits, etc).

Decreased proportion of nuclei with premature sister chromatid separation compared to controls was found on one occasion (suggestive of tighter sister chromatid cohesion) [Mullegama-A]. Sister chromatid cohesion was not affected in another report [Soardi et al.].

Western blot demonstrated significant reduction of STAG2 levels for a nonsense variant [Mullegama-A]. Levels were not perturbed for a missense variant [Soardi et al.].

Upon immunofluorescence STAG2 presented normal (nuclear) localization for a missense variant for which this was studied [Soardi et al.].

Perturbation of the cell cycle profile (higher percentage of G2/M cells) was demonstrated for patient fibroblasts compared to controls on one occasion where this was studied. [Soardi et al.].

Microarray expression studies in patient fibroblasts demonstrated altered transcription (upregulation) of genes implicated in cell division, mitosis and DNA replication upon comparison with normal fibroblasts [Soardi et al.].

The effect of a missense variant on STAG2 binding to other cohesin subunits (SCC1, SMC1 and SMC3) and regulators was studied. Binding was found to be reduced in vivo (in HeLa cells) for SCC1 (its direct binding partner) as well as SMC1, SMC3 (possibly indirectly). Reduced STAG2 binding to cohesin regulators was also shown in vivo. However, in vitro studies were not suggestive of impaired binding of STAG2 to SCC1 (a finding difficult to explain) [Soardi et al.].

STAG2 appears to be intolerant to LoF variants (pLI of 1 in ExAC). Z-Score for missense variants is 5.11.

Mullegama et al. (B) comment that Xq25 duplications in males may be associated with milder phenotypes compared to intragenic variants. They further hypothesize that males are able to survive less damaging variants while females are able to survive more deleterious (eg. LoF) ones though with more severe phenotypes (similarity to the MECP2 model is discussed).
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STAG2 is not associated with any phenotype in OMIM.
In G2P this gene is associated with STAG2-related developmental delay with microcephaly and congenital anomalies (disease confidence : confirmed / Both DD and ID among the phenotypes assigned to this entry).
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STAG2 is included in gene panels for ID offered by some diagnostic laboratories.
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As a result, this gene can be considered for inclusion in the ID panel as green (or amber).
Sources: Literature
Created: 15 Jan 2019, 1:12 a.m.

Mode of inheritance
X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)

Phenotypes
Global developmental delay; Intellectual disability; Abnormality of head or neck; Microcephaly; Growth delay; Hearing impairment; Abnormal heart morphology

Publications

Variants in this GENE are reported as part of current diagnostic practice

Created: 15 Jan 2019, 1:12 a.m.

Panel version: 2.595

Details

Mode of Inheritance
X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)
Sources
  • Expert Review Green
Phenotypes
  • STAG2-related developmental delay with microcephaly and congenital anomalies
  • STAG2-related X-linked Intellectual Deficiency
  • cohesinopathy
  • Global developmental delay
  • Intellectual disability
  • Abnormality of head or neck
  • Microcephaly
  • Growth delay
  • Hearing impairment
  • Abnormal heart morphology
OMIM
300826
Clinvar variants
Variants in STAG2
Penetrance
unknown
Publications
Panels with this gene

History Filter Activity

26 Feb 2019, Gel status: 3

Entity classified by Genomics England curator

Rebecca Foulger (Genomics England curator)

Gene: stag2 has been classified as Green List (High Evidence).

26 Feb 2019, Gel status: 0

Set mode of inheritance

Rebecca Foulger (Genomics England curator)

Mode of inheritance for gene: STAG2 was changed from X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males)

26 Feb 2019, Gel status: 0

Set Phenotypes

Rebecca Foulger (Genomics England curator)

Phenotypes for gene: STAG2 were changed from STAG2-related developmental delay with microcephaly and congenital anomalies; Global developmental delay; Intellectual disability; Abnormality of head or neck; Microcephaly; Growth delay; Hearing impairment; Abnormal heart morphology to STAG2-related developmental delay with microcephaly and congenital anomalies; STAG2-related X-linked Intellectual Deficiency; cohesinopathy; Global developmental delay; Intellectual disability; Abnormality of head or neck; Microcephaly; Growth delay; Hearing impairment; Abnormal heart morphology

26 Feb 2019, Gel status: 0

Set Phenotypes

Rebecca Foulger (Genomics England curator)

Phenotypes for gene: STAG2 were changed from Global developmental delay; Intellectual disability; Abnormality of head or neck; Microcephaly; Growth delay; Hearing impairment; Abnormal heart morphology to STAG2-related developmental delay with microcephaly and congenital anomalies; Global developmental delay; Intellectual disability; Abnormality of head or neck; Microcephaly; Growth delay; Hearing impairment; Abnormal heart morphology

15 Jan 2019, Gel status: 0

Created, Added New Source, Set mode of inheritance, Set publications, Set Phenotypes, Set penetrance

Konstantinos Varvagiannis (Other)

gene: STAG2 was added gene: STAG2 was added to Intellectual disability. Sources: Literature Mode of inheritance for gene: STAG2 was set to X-LINKED: hemizygous mutation in males, monoallelic mutations in females may cause disease (may be less severe, later onset than males) Publications for gene: STAG2 were set to 29263825; 28296084; 30158690; 30447054; 19449417; 26443594; 25677961; 23637084; 25450604 Phenotypes for gene: STAG2 were set to Global developmental delay; Intellectual disability; Abnormality of head or neck; Microcephaly; Growth delay; Hearing impairment; Abnormal heart morphology Penetrance for gene: STAG2 were set to unknown Review for gene: STAG2 was set to GREEN gene: STAG2 was marked as current diagnostic