SOX5SRY-box 5
Autism Reports / Total Reports
9 / 24Rare Variants / Common Variants
73 / 1Aliases
SOX5, L-SOX5, MGC35153Associated Syndromes
Lamb-Shaffer syndrome, Lamb-Shaffer syndrome, DD, IDChromosome Band
12p12.1Associated Disorders
ADHD, ID, ASDGenetic Category
Rare Single Gene Mutation, Syndromic, Genetic AssociationRelevance to Autism
Intragenic SOX5 deletions have been identified in an individual with ASD and individuals with developmental delay/intellectual disability (Rosenfeld et al. 2010; Lamb et al., 2012).
Molecular Function
This gene encodes a member of the SOX (SRY-related HMG-box) family of transcription factors involved in the regulation of embryonic development and in the determination of the cell fate. The encoded protein may act as a transcriptional regulator after forming a protein complex with other proteins. The encoded protein may play a role in chondrogenesis.
External Links
SFARI Genomic Platforms
Reports related to SOX5 (24 Reports)
# | Type | Title | Author, Year | Autism Report | Associated Disorders |
---|---|---|---|---|---|
1 | Primary | Copy number variations associated with autism spectrum disorders contribute to a spectrum of neurodevelopmental disorders | Rosenfeld JA , et al. (2010) | Yes | - |
2 | Support | Haploinsufficiency of SOX5 at 12p12.1 is associated with developmental delays with prominent language delay, behavior problems, and mild dysmorphic features | Lamb AN , et al. (2012) | No | ASD, ADHD |
3 | Support | Haploinsufficiency of SOX5, a member of the SOX (SRY-related HMG-box) family of transcription factors is a cause of intellectual disability | Schanze I , et al. (2012) | No | - |
4 | Support | Deletion 12p12 involving SOX5 in two children with developmental delay and dysmorphic features | Lee RW , et al. (2013) | No | - |
5 | Support | Exome sequencing expands the mechanism of SOX5-associated intellectual disability: A case presentation with review of sox-related disorders | Nesbitt A , et al. (2015) | No | - |
6 | Recent Recommendation | Meta-analysis of 2,104 trios provides support for 10 new genes for intellectual disability | Lelieveld SH et al. (2016) | No | - |
7 | Support | Mutations in Human Accelerated Regions Disrupt Cognition and Social Behavior | Doan RN , et al. (2016) | Yes | - |
8 | Support | The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies | Redin C , et al. (2016) | No | - |
9 | Support | Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder | C Yuen RK et al. (2017) | Yes | - |
10 | Support | Using medical exome sequencing to identify the causes of neurodevelopmental disorders: Experience of 2 clinical units and 216 patients | Chrot E , et al. (2017) | Yes | - |
11 | Support | Diagnostic exome sequencing of syndromic epilepsy patients in clinical practice | Tumien B , et al. (2017) | No | - |
12 | Support | Clinical and genetic characterization of a patient with SOX5 haploinsufficiency caused by a de novo balanced reciprocal translocation | Fukushi D , et al. (2018) | No | ID, autistic features |
13 | Positive Association | Common schizophrenia alleles are enriched in mutation-intolerant genes and in regions under strong background selection | Pardias AF , et al. (2018) | No | - |
14 | Recent Recommendation | Widening of the genetic and clinical spectrum of Lamb-Shaffer syndrome, a neurodevelopmental disorder due to SOX5 haploinsufficiency | Zawerton A , et al. (2019) | No | ASD |
15 | Support | - | Woodbury-Smith M et al. (2022) | Yes | - |
16 | Support | - | Zhou X et al. (2022) | Yes | - |
17 | Recent Recommendation | - | Edgerley K et al. (2023) | No | ASD or autistic features, ADHD |
18 | Support | - | Hu C et al. (2023) | Yes | - |
19 | Support | - | Wang J et al. (2023) | Yes | - |
20 | Support | - | Cirnigliaro M et al. (2023) | Yes | - |
21 | Support | - | Sanchis-Juan A et al. (2023) | No | - |
22 | Support | - | Jair Tenorio-Castano et al. (2023) | No | - |
23 | Support | - | Alistair T Pagnamenta et al. (2024) | No | - |
24 | Support | - | Axel Schmidt et al. (2024) | No | ID, cognitive impairment |
Rare Variants (73)
Status | Allele Change | Residue Change | Variant Type | Inheritance Pattern | Parental Transmission | Family Type | PubMed ID | Author, Year |
---|---|---|---|---|---|---|---|---|
- | - | translocation | De novo | - | - | 27841880 | Redin C , et al. (2016) | |
- | - | translocation | De novo | - | - | 29477873 | Fukushi D , et al. (2018) | |
- | - | copy_number_loss | Unknown | - | - | 22290657 | Lamb AN , et al. (2012) | |
- | - | copy_number_loss | De novo | - | - | 27841880 | Redin C , et al. (2016) | |
- | - | copy_number_loss | De novo | - | - | 36861937 | Edgerley K et al. (2023) | |
- | - | copy_number_loss | Unknown | - | - | 36861937 | Edgerley K et al. (2023) | |
- | - | translocation | De novo | - | Simplex | 22290657 | Lamb AN , et al. (2012) | |
- | - | copy_number_loss | De novo | - | - | 20808228 | Rosenfeld JA , et al. (2010) | |
- | - | copy_number_loss | De novo | - | Simplex | 22290657 | Lamb AN , et al. (2012) | |
- | - | copy_number_loss | De novo | - | Unknown | 22290657 | Lamb AN , et al. (2012) | |
G>A | - | stop_gained | De novo | - | Multiplex | 28263302 | C Yuen RK et al. (2017) | |
- | - | copy_number_loss | De novo | - | Simplex | 23220431 | Schanze I , et al. (2012) | |
- | - | copy_number_loss | De novo | - | Simplex | 31578471 | Zawerton A , et al. (2019) | |
- | - | copy_number_loss | Unknown | - | Simplex | 31578471 | Zawerton A , et al. (2019) | |
- | - | copy_number_loss | Familial | Maternal | - | 36861937 | Edgerley K et al. (2023) | |
c.231+14275dup | - | intron_variant | - | - | Unknown | 27667684 | Doan RN , et al. (2016) | |
c.1613C>G | p.Ser538Ter | stop_gained | De novo | - | - | 35982159 | Zhou X et al. (2022) | |
- | - | inversion | De novo | - | Simplex | 38776926 | Alistair T Pagnamenta et al. (2024) | |
- | - | copy_number_loss | Familial | Paternal | Simplex | 22290657 | Lamb AN , et al. (2012) | |
- | - | copy_number_loss | Familial | Maternal | Simplex | 31578471 | Zawerton A , et al. (2019) | |
c.1002C>T | p.Gly334%3D | synonymous_variant | De novo | - | - | 35982159 | Zhou X et al. (2022) | |
c.1895C>A | p.Thr632Asn | missense_variant | De novo | - | - | 28708303 | Chrot E , et al. (2017) | |
c.865C>T | p.Pro289Ser | missense_variant | De novo | - | - | 29286531 | Tumien B , et al. (2017) | |
c.1676C>T | p.Pro559Leu | missense_variant | De novo | - | - | 36861937 | Edgerley K et al. (2023) | |
c.1711C>T | p.Arg571Trp | missense_variant | De novo | - | - | 31578471 | Zawerton A , et al. (2019) | |
c.1786G>C | p.Ala596Pro | missense_variant | De novo | - | - | 31578471 | Zawerton A , et al. (2019) | |
c.532C>T | p.Leu178Phe | missense_variant | Familial | Maternal | - | 37007974 | Hu C et al. (2023) | |
c.472G>A | p.Glu158Lys | missense_variant | De novo | - | Simplex | 37393044 | Wang J et al. (2023) | |
c.1477C>T | p.Arg493Ter | stop_gained | De novo | - | Simplex | 36861937 | Edgerley K et al. (2023) | |
c.1534C>T | p.Gln512Ter | stop_gained | De novo | - | Simplex | 36861937 | Edgerley K et al. (2023) | |
c.622C>T | p.Gln208Ter | stop_gained | De novo | - | Simplex | 31578471 | Zawerton A , et al. (2019) | |
c.637C>T | p.Arg213Ter | stop_gained | De novo | - | Simplex | 31578471 | Zawerton A , et al. (2019) | |
c.820C>T | p.Gln274Ter | stop_gained | De novo | - | Simplex | 31578471 | Zawerton A , et al. (2019) | |
c.1234+2T>A | - | splice_site_variant | De novo | - | Simplex | 31578471 | Zawerton A , et al. (2019) | |
c.1489-1G>A | - | splice_site_variant | De novo | - | Simplex | 31578471 | Zawerton A , et al. (2019) | |
c.1814A>C | p.Tyr605Ser | missense_variant | De novo | - | - | 39039281 | Axel Schmidt et al. (2024) | |
c.1477C>T | p.Arg493Ter | stop_gained | De novo | - | Simplex | 31578471 | Zawerton A , et al. (2019) | |
c.1613C>G | p.Ser538Ter | stop_gained | De novo | - | Simplex | 31578471 | Zawerton A , et al. (2019) | |
c.1782G>A | p.Trp594Ter | stop_gained | De novo | - | Simplex | 31578471 | Zawerton A , et al. (2019) | |
c.1819G>T | p.Glu607Ter | stop_gained | De novo | - | Simplex | 31578471 | Zawerton A , et al. (2019) | |
- | - | copy_number_loss | Familial | Maternal | Multi-generational | 22290657 | Lamb AN , et al. (2012) | |
c.2051C>A | p.Ala684Asp | missense_variant | Unknown | - | - | 35205252 | Woodbury-Smith M et al. (2022) | |
c.1477C>T | p.Arg493Ter | stop_gained | Unknown | Not maternal | - | 36861937 | Edgerley K et al. (2023) | |
c.703C>T | p.Arg235Cys | missense_variant | De novo | - | Simplex | 31578471 | Zawerton A , et al. (2019) | |
c.928T>A | p.Cys310Ser | missense_variant | De novo | - | Simplex | 31578471 | Zawerton A , et al. (2019) | |
c.1678A>G | p.Met560Val | missense_variant | De novo | - | Simplex | 31578471 | Zawerton A , et al. (2019) | |
c.1712G>T | p.Arg571Leu | missense_variant | De novo | - | Simplex | 31578471 | Zawerton A , et al. (2019) | |
c.1814A>G | p.Tyr605Cys | missense_variant | De novo | - | Simplex | 31578471 | Zawerton A , et al. (2019) | |
c.1868A>G | p.Tyr623Cys | missense_variant | De novo | - | Simplex | 31578471 | Zawerton A , et al. (2019) | |
c.1895C>A | p.Thr632Asn | missense_variant | De novo | - | Simplex | 31578471 | Zawerton A , et al. (2019) | |
c.2078C>T | p.Ser693Leu | missense_variant | De novo | - | Simplex | 31578471 | Zawerton A , et al. (2019) | |
c.405dup | p.Lys136GlnfsTer6 | frameshift_variant | De novo | - | - | 39039281 | Axel Schmidt et al. (2024) | |
- | - | copy_number_loss | De novo (germline mosaicism) | - | Multiplex | 36861937 | Edgerley K et al. (2023) | |
c.1681A>C | p.Asn561His | missense_variant | De novo | - | Multiplex | 31578471 | Zawerton A , et al. (2019) | |
c.1711C>T | p.Arg571Trp | missense_variant | Unknown | - | Multiplex | 31578471 | Zawerton A , et al. (2019) | |
- | - | copy_number_loss | De novo (germline mosaicism) | - | Multiplex | 31578471 | Zawerton A , et al. (2019) | |
c.1495dup | p.Thr499AsnfsTer13 | frameshift_variant | De novo | - | - | 27479843 | Lelieveld SH et al. (2016) | |
c.1788dup | p.Met597TyrfsTer11 | frameshift_variant | De novo | - | - | 27479843 | Lelieveld SH et al. (2016) | |
c.1711C>T | p.Arg571Trp | missense_variant | Unknown | - | Simplex | 37541188 | Sanchis-Juan A et al. (2023) | |
c.622C>T | p.Gln208Ter | stop_gained | De novo | - | Multi-generational | 31578471 | Zawerton A , et al. (2019) | |
c.979-1G>A | - | splice_site_variant | Familial | Maternal | Multiplex | 37506195 | Cirnigliaro M et al. (2023) | |
c.1477C>T | p.Arg493Ter | stop_gained | Unknown | Not maternal | Simplex | 31578471 | Zawerton A , et al. (2019) | |
c.737_738insT | p.Glu246AspfsTer41 | frameshift_variant | De novo | - | - | 27479843 | Lelieveld SH et al. (2016) | |
c.1465dup | p.Leu489ProfsTer3 | frameshift_variant | De novo | - | Simplex | 31578471 | Zawerton A , et al. (2019) | |
c.1348C>T | p.Arg450Trp | missense_variant | De novo | - | Multi-generational | 31578471 | Zawerton A , et al. (2019) | |
c.1678A>G | p.Met560Val | missense_variant | De novo | - | Multi-generational | 31578471 | Zawerton A , et al. (2019) | |
c.747_748del | p.Arg250ThrfsTer36 | frameshift_variant | Unknown | - | Simplex | 31578471 | Zawerton A , et al. (2019) | |
c.518G>A | p.Trp173Ter | stop_gained | Familial | Maternal | Multi-generational | 31578471 | Zawerton A , et al. (2019) | |
c.637C>T | p.Arg213Ter | stop_gained | De novo | - | Multiplex (monozygotic twins) | 36861937 | Edgerley K et al. (2023) | |
c.1411C>T | p.Arg471Ter | stop_gained | Familial | Maternal | Multi-generational | 31578471 | Zawerton A , et al. (2019) | |
c.637C>T | p.Arg213Ter | stop_gained | De novo (germline mosaicism) | - | Multiplex | 31578471 | Zawerton A , et al. (2019) | |
c.1711C>T | p.Arg571Trp | missense_variant | De novo (germline mosaicism) | - | Multiplex | 31578471 | Zawerton A , et al. (2019) | |
c.1616_1617del | p.Glu539ValfsTer5 | frameshift_variant | De novo | - | Multiplex (monozygotic twins) | 36861937 | Edgerley K et al. (2023) |
Common Variants (1)
Status | Allele Change | Residue Change | Variant Type | Inheritance Pattern | Paternal Transmission | Family Type | PubMed ID | Author, Year |
---|---|---|---|---|---|---|---|---|
T>G | - | intergenic_variant | - | - | - | 29483656 | Pardias AF , et al. (2018) |
SFARI Gene score
High Confidence, Syndromic
Score Delta: Score remained at 1S
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."
10/1/2019
Increased from S to 1
New Scoring Scheme
Description
A SOX5 deletion was found in one ASD subject out of nearly 1500 subjects referred for clinical genetic testing (PMID 20808228). In addition, nine individuals with single-gene deletions of SOX5, of which 2 have PDD, and seven larger deletions, of which one has autism, have been found (Lamb et al., 2012). Other common associated features include ID, speech delay, dysmorphic features, and behavioral abnormalities. As a result of these initial findings and subsequent findings in patients with SOX5 variants (Schanze et al., 2013; Lee et al., 2013; Nesbitt et al., 2015), SOX5 is considered to be responsible for a neurodevelopmental disorder designated Lamb-Shaffer syndrome (OMIM 616803). As well, an additional report identified exon-including deletions and duplications of SOX5 in controls (Wong et al., 2007). Zawerton et al., 2019 collected genetic and clinical information from 41 novel patients with SOX5-associated Lamb-Shaffer syndrome and determined that, of the 25 patients evaluated for autism spectrum disorder, 6 were positively diagnosed (24%) and 11 had other behavioral disturbances including stereotypies, isolation, tantrums, and hyperactivity.
7/1/2017
Increased from S to S
Description
A SOX5 deletion was found in one ASD subject out of nearly 1500 subjects referred for clinical genetic testing (PMID 20808228). In addition, nine individuals with single-gene deletions of SOX5, of which 2 have PDD, and seven larger deletions, of which one has autism, have been found (Lamb et al., 2012). Other common associated features include ID, speech delay, dysmorphic features, and behavioral abnormalities. As a result of these initial findings and subsequent findings in patients with SOX5 variants (Schanze et al., 2013; Lee et al., 2013; Nesbitt et al., 2015), SOX5 is considered to be responsible for a neurodevelopmental disorder designated Lamb-Shaffer syndrome (OMIM 616803). As well, an additional report identified exon-including deletions and duplications of SOX5 in controls (Wong et al., 2007).
4/1/2017
Increased from S to S
Description
A SOX5 deletion was found in one ASD subject out of nearly 1500 subjects referred for clinical genetic testing (PMID 20808228). In addition, nine individuals with single-gene deletions of SOX5, of which 2 have PDD, and seven larger deletions, of which one has autism, have been found (Lamb et al., 2012). Other common associated features include ID, speech delay, dysmorphic features, and behavioral abnormalities. As a result of these initial findings and subsequent findings in patients with SOX5 variants (Schanze et al., 2013; Lee et al., 2013; Nesbitt et al., 2015), SOX5 is considered to be responsible for a neurodevelopmental disorder designated Lamb-Shaffer syndrome (OMIM 616803). As well, an additional report identified exon-including deletions and duplications of SOX5 in controls (Wong et al., 2007).
Reports Added
[Copy number variations associated with autism spectrum disorders contribute to a spectrum of neurodevelopmental disorders.2010] [Haploinsufficiency of SOX5 at 12p12.1 is associated with developmental delays with prominent language delay, behavior problems, and mild dysmorphic...2012] [Haploinsufficiency of SOX5, a member of the SOX (SRY-related HMG-box) family of transcription factors is a cause of intellectual disability.2012] [Meta-analysis of 2,104 trios provides support for 10 new genes for intellectual disability2016] [Mutations in Human Accelerated Regions Disrupt Cognition and Social Behavior.2016] [The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies.2016] [Haploinsufficiency of SOX5, a member of the SOX (SRY-related HMG-box) family of transcription factors is a cause of intellectual disability.2012] [Deletion 12p12 involving SOX5 in two children with developmental delay and dysmorphic features.2013] [Exome sequencing expands the mechanism of SOX5-associated intellectual disability: A case presentation with review of sox-related disorders.2015] [Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder2017]1/1/2017
Decreased from 4 to S
Description
A SOX5 deletion was found in one ASD subject out of nearly 1500 subjects referred for clinical genetic testing (PMID 20808228). In addition, nine individuals with single-gene deletions of SOX5, of which 2 have PDD, and seven larger deletions, of which one has autism, have been found (Lamb et al., 2012). Other common associated features include ID, speech delay, dysmorphic features, and behavioral abnormalities. As a result of these initial findings and subsequent findings in patients with SOX5 variants (Schanze et al., 2013; Lee et al., 2013; Nesbitt et al., 2015), SOX5 is considered to be responsible for a neurodevelopmental disorder designated Lamb-Shaffer syndrome (OMIM 616803). As well, an additional report identified exon-including deletions and duplications of SOX5 in controls (Wong et al., 2007).
10/1/2016
Decreased from 4 to 4
Description
A SOX5 deletion was found in one ASD subject out of nearly 1500 subjects referred for clinical genetic testing (PMID 20808228). In addition, nine individuals with single-gene deletions of SOX5, of which 2 have PDD, and seven larger deletions, of which one has autism, have been found (PMID 22290657). Other common associated features include ID, speech delay, dysmorphic features, and behavioral abnormalities. As well, an additional report exists that found exon-including deletion and duplication of SOX5 in controls (Wong et al., 2007).
7/1/2016
Decreased from 4 to 4
Description
A SOX5 deletion was found in one ASD subject out of nearly 1500 subjects referred for clinical genetic testing (PMID 20808228). In addition, nine individuals with single-gene deletions of SOX5, of which 2 have PDD, and seven larger deletions, of which one has autism, have been found (PMID 22290657). Other common associated features include ID, speech delay, dysmorphic features, and behavioral abnormalities. As well, an additional report exists that found exon-including deletion and duplication of SOX5 in controls (Wong et al., 2007).
7/1/2014
Increased from No data to 4
Description
A SOX5 deletion was found in one ASD subject out of nearly 1500 subjects referred for clinical genetic testing (PMID 20808228). In addition, nine individuals with single-gene deletions of SOX5, of which 2 have PDD, and seven larger deletions, of which one has autism, have been found (PMID 22290657). Other common associated features include ID, speech delay, dysmorphic features, and behavioral abnormalities. As well, an additional report exists that found exon-including deletion and duplication of SOX5 in controls (Wong et al., 2007).
4/1/2014
Increased from No data to 4
Description
A SOX5 deletion was found in one ASD subject out of nearly 1500 subjects referred for clinical genetic testing (PMID 20808228). In addition, nine individuals with single-gene deletions of SOX5, of which 2 have PDD, and seven larger deletions, of which one has autism, have been found (PMID 22290657). Other common associated features include ID, speech delay, dysmorphic features, and behavioral abnormalities. As well, an additional report exists that found exon-including deletion and duplication of SOX5 in controls (Wong et al., 2007).
Krishnan Probability Score
Score 0.57254780058653
Ranking 704/25841 scored genes
[Show Scoring Methodology]
ExAC Score
Score 0.99939888448761
Ranking 971/18225 scored genes
[Show Scoring Methodology]
Sanders TADA Score
Score 0.94944162089237
Ranking 18092/18665 scored genes
[Show Scoring Methodology]
Zhang D Score
Score 0.16599059168542
Ranking 4873/20870 scored genes
[Show Scoring Methodology]
Interactome
- Protein Binding
- DNA Binding
- RNA Binding
- Protein Modification
- Direct Regulation
- ASD-Linked Genes
Interaction Table
Interactor Symbol | Interactor Name | Interactor Organism | Interactor Type | Entrez ID | Uniprot ID |
---|---|---|---|---|---|
FAM46B | family with sequence similarity 46, member B | Human | Protein Binding | 115572 | Q96A09 |
SOX1 | Transcription factor SOX-1 | Human | Protein Binding | 6656 | O00570 |