SMC3structural maintenance of chromosomes 3
Autism Reports / Total Reports
6 / 14Rare Variants / Common Variants
27 / 0Aliases
SMC3, BAM, BMH, CDLS3, CSPG6, HCAPL1, SMC3Associated Syndromes
Cornelia de Lange syndrome-3 (CDLS3)Chromosome Band
10q25.2Associated Disorders
-Relevance to Autism
A de novo likely gene disruptive (LGD) variant in SMC3 was identified in an ASD proband from the Autism Simplex Collection in Stessman et al., 2017. Mutations in the SMC3 gene are associated with a form of Cornelia de Lange syndrome (Cornelia de Lange syndrome 3; OMIM 610759) (Deardorff et al., 2007; Gil-Rodrguez et al., 2015). Phenotypic characterization of 16 patients with Cornelia de Lange-like features caused by SMC3 variants in Gil-Rodrguez et al., 2015 demonstrated that, while intellectual disability was a prominent feature, behavioral problems were less frequently reported (1 individual presented with autism, whereas another presented with autistic features; poor eye contact, attention deficit disorder, aggression, and self-injurious behavior were also observed).
Molecular Function
Central component of cohesin, a complex required for chromosome cohesion during the cell cycle.
External Links
SFARI Genomic Platforms
Reports related to SMC3 (14 Reports)
# | Type | Title | Author, Year | Autism Report | Associated Disorders |
---|---|---|---|---|---|
1 | Highly Cited | Mutations in cohesin complex members SMC3 and SMC1A cause a mild variant of cornelia de Lange syndrome with predominant mental retardation | Deardorff MA , et al. (2007) | No | - |
2 | Primary | The contribution of de novo coding mutations to autism spectrum disorder | Iossifov I et al. (2014) | Yes | - |
3 | Support | Large-scale discovery of novel genetic causes of developmental disorders | Deciphering Developmental Disorders Study (2014) | No | - |
4 | Support | De novo heterozygous mutations in SMC3 cause a range of Cornelia de Lange syndrome-overlapping phenotypes | Gil-Rodrguez MC , et al. (2015) | No | - |
5 | Recent Recommendation | Targeted sequencing identifies 91 neurodevelopmental-disorder risk genes with autism and developmental-disability biases | Stessman HA , et al. (2017) | Yes | - |
6 | Support | Genomic diagnosis for children with intellectual disability and/or developmental delay | Bowling KM , et al. (2017) | No | - |
7 | Recent Recommendation | Diagnosis and management of Cornelia de Lange syndrome: first international consensus statement | Kline AD , et al. (2018) | No | - |
8 | Support | Whole genome sequencing and variant discovery in the ASPIRE autism spectrum disorder cohort | Callaghan DB , et al. (2019) | Yes | - |
9 | Support | Diagnostic Yields of Trio-WES Accompanied by CNVseq for Rare Neurodevelopmental Disorders | Gao C , et al. (2019) | No | - |
10 | Support | - | Mahjani B et al. (2021) | Yes | - |
11 | Support | - | Zhou X et al. (2022) | Yes | - |
12 | Support | - | Spataro N et al. (2023) | No | - |
13 | Support | - | Wang J et al. (2023) | Yes | - |
14 | Support | - | Morad Ansari et al. (2024) | No | ASD, ADD, ADHD, ID, epilepsy/seizures |
Rare Variants (27)
Status | Allele Change | Residue Change | Variant Type | Inheritance Pattern | Parental Transmission | Family Type | PubMed ID | Author, Year |
---|---|---|---|---|---|---|---|---|
- | - | copy_number_loss | De novo | - | - | 38297832 | Morad Ansari et al. (2024) | |
- | - | copy_number_loss | Familial | Paternal | - | 38297832 | Morad Ansari et al. (2024) | |
- | - | copy_number_loss | Unknown | Not maternal | - | 38297832 | Morad Ansari et al. (2024) | |
c.430-1G>T | - | splice_site_variant | De novo | - | - | 38297832 | Morad Ansari et al. (2024) | |
c.2372T>G | p.Leu791Trp | missense_variant | De novo | - | - | 35982159 | Zhou X et al. (2022) | |
c.778C>T | p.Gln260Ter | stop_gained | De novo | - | - | 38297832 | Morad Ansari et al. (2024) | |
c.1561C>T | p.Arg521Ter | stop_gained | Unknown | - | - | 38297832 | Morad Ansari et al. (2024) | |
c.2899C>T | p.Arg967Ter | stop_gained | De novo | - | - | 38297832 | Morad Ansari et al. (2024) | |
c.324G>C | p.Gln108His | missense_variant | Unknown | - | - | 34615535 | Mahjani B et al. (2021) | |
c.283G>A | p.Glu95Lys | missense_variant | De novo | - | - | 28554332 | Bowling KM , et al. (2017) | |
c.2062_2064del | p.Glu688del | inframe_deletion | De novo | - | - | 35982159 | Zhou X et al. (2022) | |
c.2005_2007del | p.Tyr669del | inframe_deletion | De novo | - | - | 36980980 | Spataro N et al. (2023) | |
c.661C>T | p.Arg221Ter | stop_gained | Familial | Maternal | - | 38297832 | Morad Ansari et al. (2024) | |
c.3035A>T | p.Lys1012Ile | missense_variant | De novo | - | Multiplex | 35982159 | Zhou X et al. (2022) | |
c.1078C>T | p.Arg360Ter | stop_gained | Familial | Paternal | - | 38297832 | Morad Ansari et al. (2024) | |
c.2413C>T | p.Arg805Cys | missense_variant | De novo | - | Simplex | 25363768 | Iossifov I et al. (2014) | |
c.1464_1466del | p.Glu488del | inframe_deletion | De novo | - | - | 17273969 | Deardorff MA , et al. (2007) | |
c.3002_3004del | p.Ile1001del | inframe_deletion | De novo | - | Simplex | 37393044 | Wang J et al. (2023) | |
c.1071_1074del | p.Glu358AsnfsTer44 | frameshift_variant | De novo | - | - | 31178897 | Gao C , et al. (2019) | |
c.461dup | p.Arg155GlufsTer12 | frameshift_variant | Unknown | - | - | 38297832 | Morad Ansari et al. (2024) | |
c.1539del | p.Asn513LysfsTer4 | frameshift_variant | Unknown | - | - | 38297832 | Morad Ansari et al. (2024) | |
c.1892T>C | p.Leu631Pro | missense_variant | Unknown | - | Simplex | 31038196 | Callaghan DB , et al. (2019) | |
c.1474_1478del | p.Lys492AlafsTer5 | frameshift_variant | De novo | - | - | 38297832 | Morad Ansari et al. (2024) | |
c.3646_3647dup | p.Gly1217MetfsTer39 | frameshift_variant | Unknown | - | - | 38297832 | Morad Ansari et al. (2024) | |
c.2412dup | p.Arg805SerfsTer13 | frameshift_variant | De novo | - | Simplex | 28191889 | Stessman HA , et al. (2017) | |
TGAAAAGAA>TGAA | - | frameshift_variant | De novo | - | - | 25533962 | Deciphering Developmental Disorders Study (2014) | |
c.3563G>C | p.Gly1188Ala | missense_variant | De novo | - | - | 25533962 | Deciphering Developmental Disorders Study (2014) |
Common Variants
No common variants reported.
SFARI Gene score
Strong Candidate, Syndromic
![](https://gene.sfari.org//wp-content/themes/sfari-gene/img/color-band/2.png)
![](https://gene.sfari.org//wp-content/themes/sfari-gene/img/color-band/s.png)
A de novo likely gene disruptive (LGD) variant in SMC3 was identified in an ASD proband from the Autism Simplex Collection in Stessman et al., 2017. Mutations in the SMC3 gene are associated with a form of Cornelia de Lange syndrome (Cornelia de Lange syndrome 3; OMIM 610759) (Deardorff et al., 2007; Gil-Rodrguez et al., 2015). Phenotypic characterization of 16 patients with Cornelia de Lange-like features caused by SMC3 variants in Gil-Rodrguez et al., 2015 demonstrated that, while intellectual disability was a prominent feature, behavioral problems were less frequently reported (1 individual presented with autism, whereas another presented with autistic features; poor eye contact, attention deficit disorder, aggression, and self-injurious behavior were also observed). A comparison of the primary clinical findings in individuals with molecularly confirmed Cornelia de Lange syndrome in Kline et al., 2018 determined that 20-49% of individuals with SMC3 mutations presented with autism spectrum disorder.
Score Delta: Score remained at 2S
criteria met
See SFARI Gene'scoring criteriaWe considered a rigorous statistical comparison between cases and controls, yielding genome-wide statistical significance, with independent replication, to be the strongest possible evidence for a gene. These criteria were relaxed slightly for category 2.
The syndromic category includes mutations that are associated with a substantial degree of increased risk and consistently linked to additional characteristics not required for an ASD diagnosis. If there is independent evidence implicating a gene in idiopathic ASD, it will be listed as "#S" (e.g., 2S, 3S, etc.). If there is no such independent evidence, the gene will be listed simply as "S."
4/1/2022
![icon](https://gene.sfari.org//wp-content/themes/sfari-gene/img/score-down.png)
Decreased from 3S to 2S
Description
A de novo likely gene disruptive (LGD) variant in SMC3 was identified in an ASD proband from the Autism Simplex Collection in Stessman et al., 2017. Mutations in the SMC3 gene are associated with a form of Cornelia de Lange syndrome (Cornelia de Lange syndrome 3; OMIM 610759) (Deardorff et al., 2007; Gil-Rodrguez et al., 2015). Phenotypic characterization of 16 patients with Cornelia de Lange-like features caused by SMC3 variants in Gil-Rodrguez et al., 2015 demonstrated that, while intellectual disability was a prominent feature, behavioral problems were less frequently reported (1 individual presented with autism, whereas another presented with autistic features; poor eye contact, attention deficit disorder, aggression, and self-injurious behavior were also observed). A comparison of the primary clinical findings in individuals with molecularly confirmed Cornelia de Lange syndrome in Kline et al., 2018 determined that 20-49% of individuals with SMC3 mutations presented with autism spectrum disorder.
10/1/2019
![icon](https://gene.sfari.org//wp-content/themes/sfari-gene/img/score-down.png)
Decreased from 4S to 3S
New Scoring Scheme
Description
A de novo likely gene disruptive (LGD) variant in SMC3 was identified in an ASD proband from the Autism Simplex Collection in Stessman et al., 2017. Mutations in the SMC3 gene are associated with a form of Cornelia de Lange syndrome (Cornelia de Lange syndrome 3; OMIM 610759) (Deardorff et al., 2007; Gil-Rodrguez et al., 2015). Phenotypic characterization of 16 patients with Cornelia de Lange-like features caused by SMC3 variants in Gil-Rodrguez et al., 2015 demonstrated that, while intellectual disability was a prominent feature, behavioral problems were less frequently reported (1 individual presented with autism, whereas another presented with autistic features; poor eye contact, attention deficit disorder, aggression, and self-injurious behavior were also observed). A comparison of the primary clinical findings in individuals with molecularly confirmed Cornelia de Lange syndrome in Kline et al., 2018 determined that 20-49% of individuals with SMC3 mutations presented with autism spectrum disorder.
Reports Added
[New Scoring Scheme]7/1/2019
![icon](https://gene.sfari.org//wp-content/themes/sfari-gene/img/score-same.png)
Decreased from 4S to 4S
Description
A de novo likely gene disruptive (LGD) variant in SMC3 was identified in an ASD proband from the Autism Simplex Collection in Stessman et al., 2017. Mutations in the SMC3 gene are associated with a form of Cornelia de Lange syndrome (Cornelia de Lange syndrome 3; OMIM 610759) (Deardorff et al., 2007; Gil-Rodrguez et al., 2015). Phenotypic characterization of 16 patients with Cornelia de Lange-like features caused by SMC3 variants in Gil-Rodrguez et al., 2015 demonstrated that, while intellectual disability was a prominent feature, behavioral problems were less frequently reported (1 individual presented with autism, whereas another presented with autistic features; poor eye contact, attention deficit disorder, aggression, and self-injurious behavior were also observed). A comparison of the primary clinical findings in individuals with molecularly confirmed Cornelia de Lange syndrome in Kline et al., 2018 determined that 20-49% of individuals with SMC3 mutations presented with autism spectrum disorder.
4/1/2019
![icon](https://gene.sfari.org//wp-content/themes/sfari-gene/img/score-same.png)
Decreased from 4S to 4S
Description
A de novo likely gene disruptive (LGD) variant in SMC3 was identified in an ASD proband from the Autism Simplex Collection in Stessman et al., 2017. Mutations in the SMC3 gene are associated with a form of Cornelia de Lange syndrome (Cornelia de Lange syndrome 3; OMIM 610759) (Deardorff et al., 2007; Gil-Rodrguez et al., 2015). Phenotypic characterization of 16 patients with Cornelia de Lange-like features caused by SMC3 variants in Gil-Rodrguez et al., 2015 demonstrated that, while intellectual disability was a prominent feature, behavioral problems were less frequently reported (1 individual presented with autism, whereas another presented with autistic features; poor eye contact, attention deficit disorder, aggression, and self-injurious behavior were also observed). A comparison of the primary clinical findings in individuals with molecularly confirmed Cornelia de Lange syndrome in Kline et al., 2018 determined that 20-49% of individuals with SMC3 mutations presented with autism spectrum disorder.
7/1/2018
![icon](https://gene.sfari.org//wp-content/themes/sfari-gene/img/score-same.png)
Decreased from 4S to 4S
Description
A de novo likely gene disruptive (LGD) variant in SMC3 was identified in an ASD proband from the Autism Simplex Collection in Stessman et al., 2017. Mutations in the SMC3 gene are associated with a form of Cornelia de Lange syndrome (Cornelia de Lange syndrome 3; OMIM 610759) (Deardorff et al., 2007; Gil-Rodrguez et al., 2015). Phenotypic characterization of 16 patients with Cornelia de Lange-like features caused by SMC3 variants in Gil-Rodrguez et al., 2015 demonstrated that, while intellectual disability was a prominent feature, behavioral problems were less frequently reported (1 individual presented with autism, whereas another presented with autistic features; poor eye contact, attention deficit disorder, aggression, and self-injurious behavior were also observed). A comparison of the primary clinical findings in individuals with molecularly confirmed Cornelia de Lange syndrome in Kline et al., 2018 determined that 20-49% of individuals with SMC3 mutations presented with autism spectrum disorder.
7/1/2017
![icon](https://gene.sfari.org//wp-content/themes/sfari-gene/img/score-same.png)
Decreased from 4 to 4S
Description
A de novo likely gene disruptive (LGD) variant in SMC3 was identified in an ASD proband from the Autism Simplex Collection in Stessman et al., 2017. Mutations in the SMC3 gene are associated with a form of Cornelia de Lange syndrome (Cornelia de Lange syndrome 3; OMIM 610759) (Deardorff et al., 2007; Gil-RodrÃguez et al., 2015). Phenotypic characterization of 16 patients with Cornelia de Lange-like features caused by SMC3 variants in Gil-RodrÃguez et al., 2015 demonstrated that, while intellectual disability was a prominent feature, behavioral problems were less frequently reported (1 individual presented with autism, whereas another presented with autistic features; poor eye contact, attention deficit disorder, aggression, and self-injurious behavior were also observed).
1/1/2017
![icon](https://gene.sfari.org//wp-content/themes/sfari-gene/img/score-up.png)
Increased from to 4
Description
A de novo likely gene disruptive (LGD) variant in SMC3 was identified in an ASD proband from the Autism Simplex Collection in Stessman et al., 2017.
Krishnan Probability Score
Score 0.50168859867179
Ranking 2009/25841 scored genes
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ExAC Score
Score 0.99999999949759
Ranking 88/18225 scored genes
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Sanders TADA Score
Score 0.79349148547812
Ranking 2100/18665 scored genes
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Zhang D Score
Score 0.35025904787074
Ranking 2005/20870 scored genes
[Show Scoring Methodology]