Summary Statistics:
ASD Reports: 16
Recent Reports: 3
Annotated variants: 97
Associated CNVs: 8
Evidence score: 5
Gene Score: 3
Relevance to Autism
De novo likely gene-disruptive (LGD) variants in the SPEN gene have been identified in two probands with ASD (Iossifov et al., 2014; Yuen et al., 2016) and two probands with unspecified developmental disorders (Deciphering Developmental Disorders Study 2017). An integrated meta-analysis of de novo mutation data from a combined dataset of 10,927 individuals with neurodevelopmental disorders identified SPEN as a gene with an excess of LGD variants (false discovery rata < 5%, count >1) (Coe et al., 2018). De novo missense variants in SPEN have also been observed in ASD probands (De Rubeis et al., 2014; Iossifov et al., 2014; Krumm et al., 2015).
Molecular Function
his gene encodes a hormone inducible transcriptional repressor. Repression of transcription by this gene product can occur through interactions with other repressors, by the recruitment of proteins involved in histone deacetylation, or through sequestration of transcriptional activators. The product of this gene contains a carboxy-terminal domain that permits binding to other corepressor proteins. This domain also permits interaction with members of the NuRD complex, a nucleosome remodeling protein complex that contains deacetylase activity. In addition, this repressor contains several RNA recognition motifs that confer binding to a steroid receptor RNA coactivator; this binding can modulate the activity of both liganded and nonliganded steroid receptors.
References
Primary
The contribution of de novo coding mutations to autism spectrum disorder
ASD
Support
Excess of rare, inherited truncating mutations in autism.
ASD
Support
Combining exome/genome sequencing with data repository analysis reveals novel gene-disease associations for a wide range of genetic disorders
DD, ID
Support
Synaptic, transcriptional and chromatin genes disrupted in autism.
ASD
Support
Rare genetic susceptibility variants assessment in autism spectrum disorder: detection rate and practical use.
ASD
Support
Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism
ASD
Support
ASD
Learning disability, epilepsy/seizures
Support
Lessons Learned from Large-Scale, First-Tier Clinical Exome Sequencing in a Highly Consanguineous Population.
ID, speech delay, motor delay
Autistic features
Support
DD, ID
Autistic features
Support
Prevalence and architecture of de novo mutations in developmental disorders
DD
Support
Integrating de novo and inherited variants in 42
ASD
Support
Genome-wide characteristics of de novo mutations in autism
ASD
Support
Mutational Landscape of Autism Spectrum Disorder Brain Tissue
ASD
Recent recommendation
SPEN haploinsufficiency causes a neurodevelopmental disorder overlapping proximal 1p36 deletion syndrome with an episignature of X chromosomes in females
DD, ID
ASD
Recent Recommendation
Large-scale targeted sequencing identifies risk genes for neurodevelopmental disorders
ASD, DD
Recent Recommendation
Neurodevelopmental disease genes implicated by de novo mutation and copy number variation morbidity.
GEN1061R001
frameshift_variant
c.3029dup
p.Asp1011GlyfsTer11
De novo
Simplex
GEN1061R002
missense_variant
c.8492G>C
p.Ser2831Thr
De novo
Simplex
GEN1061R003
missense_variant
c.986A>C
p.Asp329Ala
De novo
GEN1061R004
missense_variant
c.4651G>A
p.Glu1551Lys
De novo
Simplex
GEN1061R005
stop_gained
c.5392C>T
p.Gln1798Ter
De novo
Simplex
GEN1061R006
stop_gained
c.7503G>A
p.Trp2501Ter
De novo
GEN1061R007
frameshift_variant
c.6959_6963del
p.Glu2320GlyfsTer37
De novo
GEN1061R008
missense_variant
c.461G>A
p.Arg154Gln
De novo
GEN1061R009
missense_variant
c.4054G>A
p.Asp1352Asn
Unknown
Unknown
GEN1061R010
missense_variant
c.10093C>T
p.Pro3365Ser
De novo
Simplex
GEN1061R011
stop_gained
c.7232C>A
p.Ser2411Ter
De novo
Simplex
GEN1061R012
missense_variant
c.2137C>T
p.Arg713Trp
De novo
GEN1061R013
frameshift_variant
c.6960del
p.Val2321TrpfsTer32
De novo
GEN1061R014
splice_site_variant
c.10864-1G>A
Familial
Paternal
GEN1061R015
frameshift_variant
c.4441_4444del
p.Glu1481ArgfsTer14
Unknown
GEN1061R016
stop_gained
c.5392C>T
p.Gln1798Ter
Unknown
Not paternal
Simplex
GEN1061R017
missense_variant
c.460C>T
p.Arg154Trp
Familial
Maternal
GEN1061R018
missense_variant
c.526C>T
p.Arg176Trp
Unknown
GEN1061R019
missense_variant
c.526C>T
p.Arg176Trp
Unknown
GEN1061R020
missense_variant
c.5533G>A
p.Glu1845Lys
Unknown
GEN1061R021
missense_variant
c.5533G>A
p.Glu1845Lys
Unknown
GEN1061R022
missense_variant
c.1700C>A
p.Ala567Glu
Unknown
GEN1061R023
missense_variant
c.2612G>A
p.Arg871His
Unknown
GEN1061R024
missense_variant
c.2959C>T
p.Arg987Cys
Unknown
GEN1061R025
missense_variant
c.6995G>A
p.Arg2332His
Unknown
GEN1061R026
missense_variant
c.923G>T
p.Arg308Leu
Familial
Paternal
GEN1061R027
missense_variant
c.1379G>A
p.Arg460His
Familial
Paternal
GEN1061R028
missense_variant
c.2429G>A
p.Arg810Gln
Familial
Paternal
GEN1061R029
missense_variant
c.1703C>T
p.Ala568Val
Unknown
GEN1061R030
missense_variant
c.10301C>T
p.Pro3434Leu
Unknown
GEN1061R031
missense_variant
c.4801G>A
p.Asp1601Asn
Unknown
Not maternal
GEN1061R032
missense_variant
c.1649G>A
p.Arg550His
Unknown
GEN1061R033
missense_variant
c.1649G>A
p.Arg550His
Unknown
GEN1061R034
missense_variant
c.1649G>A
p.Arg550His
Unknown
GEN1061R035
frameshift_variant
c.2294_2295del
p.Ser765MetfsTer2
De novo
GEN1061R036
stop_gained
c.9502C>T
p.Arg3168Ter
Familial
Paternal
GEN1061R037
frameshift_variant
c.7080_7083del
p.Asn2360LysfsTer42
Unknown
Simplex
GEN1061R038
stop_gained
c.3721C>T
p.Arg1241Ter
Unknown
GEN1061R039
stop_gained
c.4207C>T
p.Arg1403Ter
Unknown
GEN1061R040
missense_variant
c.686G>A
p.Arg229Gln
Unknown
GEN1061R041
missense_variant
c.686G>A
p.Arg229Gln
Unknown
GEN1061R042
missense_variant
c.4783C>A
p.Gln1595Lys
Unknown
GEN1061R043
missense_variant
c.4783C>A
p.Gln1595Lys
Unknown
GEN1061R044
missense_variant
c.577C>T
p.Arg193Cys
Unknown
GEN1061R045
missense_variant
c.598C>G
p.Arg200Gly
Unknown
GEN1061R046
missense_variant
c.703C>T
p.Arg235Trp
Unknown
GEN1061R047
missense_variant
c.1475C>G
p.Ala492Gly
Unknown
GEN1061R048
missense_variant
c.1958G>C
p.Arg653Pro
Unknown
GEN1061R049
missense_variant
c.2137C>T
p.Arg713Trp
Unknown
GEN1061R050
missense_variant
c.4246C>T
p.Arg1416Cys
Unknown
GEN1061R051
missense_variant
c.4774C>T
p.Arg1592Trp
Unknown
GEN1061R052
missense_variant
c.6242G>A
p.Arg2081Gln
Unknown
GEN1061R053
missense_variant
c.382C>T
p.Arg128Cys
Unknown
GEN1061R054
missense_variant
c.2341C>T
p.Arg781Cys
Unknown
GEN1061R055
missense_variant
c.727C>T
p.Arg243Trp
Unknown
GEN1061R056
missense_variant
c.1649G>T
p.Arg550Leu
Unknown
GEN1061R057
missense_variant
c.10927G>A
p.Ala3643Thr
Unknown
GEN1061R058
missense_variant
c.1889G>A
p.Arg630His
Unknown
Not maternal
GEN1061R059
stop_gained
c.6058C>T
p.Gln2020Ter
De novo
GEN1061R060
frameshift_variant
c.6087_6088del
p.Glu2029AspfsTer5
De novo
GEN1061R061
frameshift_variant
c.7338_7339dup
p.Arg2447ThrfsTer14
De novo
GEN1061R062
stop_gained
c.2014C>T
p.Arg672Ter
De novo
GEN1061R063
stop_gained
c.7324G>T
p.Glu2442Ter
De novo
GEN1061R064
stop_gained
c.5806C>T
p.Arg1936Ter
Familial
Maternal
Multiplex
GEN1061R065
frameshift_variant
c.7492del
p.Val2498Ter
De novo
GEN1061R066
frameshift_variant
c.6223_6227del
p.Ser2075GlufsTer46
De novo
GEN1061R067
stop_gained
c.7024C>T
p.Arg2342Ter
De novo
GEN1061R068
stop_gained
c.3793C>T
p.Arg1265Ter
De novo
GEN1061R069
frameshift_variant
c.6226_6227del
p.Lys2076GlufsTer46
De novo
GEN1061R070
frameshift_variant
c.6974_6975del
p.Leu2325ArgfsTer33
De novo
GEN1061R071
stop_gained
c.3793C>T
p.Arg1265Ter
De novo
GEN1061R072
frameshift_variant
c.7374_7381del
p.Val2459ThrfsTer36
De novo
GEN1061R073
frameshift_variant
c.7373del
p.Pro2458ArgfsTer2
De novo
GEN1061R074
stop_gained
c.1603C>T
p.Arg535Ter
De novo
GEN1061R075
frameshift_variant
c.6570dup
p.Lys2191Ter
De novo
GEN1061R076
frameshift_variant
c.7328del
p.Glu2443GlyfsTer17
Familial
Paternal
Multiplex
GEN1061R077
frameshift_variant
c.2956_2959dup
p.Arg987GlnfsTer36
De novo
GEN1061R078
frameshift_variant
c.9950dup
p.Ala3318GlyfsTer30
De novo
GEN1061R079
frameshift_variant
c.10909_10910del
p.His3638ProfsTer7
De novo
GEN1061R080
frameshift_variant
c.5013_5017del
p.Glu1671AspfsTer16
De novo
GEN1061R081
frameshift_variant
c.2269_2272dup
p.Arg758GlnfsTer11
De novo
GEN1061R082
frameshift_variant
c.10953dup
p.Asn3652GlnfsTer17
De novo
GEN1061R083
frameshift_variant
c.5414del
p.Leu1805Ter
De novo
GEN1061R084
frameshift_variant
c.2262_2265dup
p.Tyr756AlafsTer13
Unknown
GEN1061R085
frameshift_variant
c.6641_6642del
p.Glu2214AlafsTer11
De novo
GEN1061R086
stop_gained
c.6799G>T
p.Glu2267Ter
Unknown
Not maternal
GEN1061R087
stop_gained
c.2101G>T
p.Glu701Ter
De novo
GEN1061R088
stop_gained
c.3508C>T
p.Arg1170Ter
De novo
GEN1061R089
stop_gained
c.3199C>T
p.Gln1067Ter
De novo
GEN1061R090
frameshift_variant
c.3029dup
p.Asp1011GlyfsTer11
De novo
GEN1061R091
stop_gained
c.5392C>T
p.Gln1798Ter
Unknown
Not paternal
GEN1061R092
stop_gained
c.5086C>T
p.Gln1696Ter
De novo
Simplex
GEN1061R093
missense_variant
c.7712C>T
p.Ala2571Val
Unknown
GEN1061R094
missense_variant
c.7796C>T
p.Ser2599Leu
Unknown
GEN1061R095
synonymous_variant
c.6750C>T
p.Pro2250%3D
De novo
GEN1061R096
stop_gained
c.4828C>T
p.Gln1610Ter
De novo
GEN1061R097
inframe_deletion
c.7380_7382del
p.Pro2462del
De novo
Multiplex
No Common Variants Available
No Animal Model Data Available
No Interactions Available