AUTS2

gene
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Also known as KIAA0442FBRSL2

Summary

AUTS2 (activator of transcription and developmental regulator AUTS2, HGNC:14262) is a protein-coding gene on chromosome 7q11.22, encoding Autism susceptibility gene 2 protein (Q8WXX7). Component of a Polycomb group (PcG) multiprotein PRC1-like complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. It is haploinsufficient (ClinGen: sufficient evidence).

This gene has been implicated in neurodevelopment and as a candidate gene for numerous neurological disorders, including autism spectrum disorders, intellectual disability, and developmental delay. Mutations in this gene have also been associated with non-neurological disorders, such as acute lymphoblastic leukemia, aging of the skin, early-onset androgenetic alopecia, and certain cancers. Alternative splicing results in multiple transcript variants encoding different isoforms.

Source: NCBI Gene 26053 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): syndromic intellectual disability (Definitive, ClinGen) — +1 more curated relationship
  • GWAS associations: 57
  • Clinical variants (ClinVar): 1,416 total — 114 pathogenic, 48 likely-pathogenic
  • Phenotypes (HPO): 70
  • Dosage sensitivity (ClinGen): haploinsufficiency sufficient evidence, triplosensitivity no evidence
  • MANE Select transcript: NM_015570

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:14262
Approved symbolAUTS2
Nameactivator of transcription and developmental regulator AUTS2
Location7q11.22
Locus typegene with protein product
StatusApproved
AliasesKIAA0442, FBRSL2
Ensembl geneENSG00000158321
Ensembl biotypeprotein_coding
OMIM607270
Entrez26053

Gene structure

Transcript identifiers

Ensembl transcripts: 34 — 16 protein_coding, 10 retained_intron, 4 protein_coding_CDS_not_defined, 4 nonsense_mediated_decay

ENST00000342771, ENST00000403018, ENST00000406775, ENST00000416482, ENST00000418686, ENST00000439256, ENST00000443672, ENST00000449547, ENST00000464768, ENST00000465899, ENST00000475660, ENST00000476695, ENST00000481994, ENST00000483297, ENST00000489774, ENST00000498384, ENST00000611706, ENST00000615871, ENST00000643060, ENST00000643587, ENST00000643936, ENST00000644359, ENST00000644506, ENST00000644939, ENST00000644949, ENST00000646136, ENST00000646193, ENST00000647121, ENST00000647140, ENST00000656200, ENST00000656998, ENST00000659051, ENST00000664521, ENST00000700075

RefSeq mRNA: 3 — MANE Select: NM_015570 NM_001127231, NM_001127232, NM_015570

CCDS: CCDS47601, CCDS47602, CCDS5539

Canonical transcript exons

ENST00000342771 — 19 exons

ExonStartEnd
ENSE000010383697078720970787431
ENSE000010908637076287070763341
ENSE000013117717076475270765005
ENSE000013161697069856970698620
ENSE000013264697043575270435781
ENSE000016629746959847569599962
ENSE000034672647078595570786038
ENSE000034780607077402870774099
ENSE000034953117078161570781756
ENSE000035013957011813270118233
ENSE000035370687078494270785019
ENSE000035493527013453670134571
ENSE000035559107077154970771644
ENSE000035803307077535770775386
ENSE000036054166989928669899498
ENSE000036159957076611470766334
ENSE000036194737077710370777174
ENSE000036215277076802470768068
ENSE000038303147078974870793506

Expression profiles

Bgee: expression breadth ubiquitous, 292 present calls, max score 99.22.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 30.4732 / max 635.2414, expressed in 1508 samples.

FANTOM5 promoters (33 alternative TSS)

Promoter IDTPM avgSamples expressed
7896313.23881325
789232.2649761
789652.1616847
789242.1571757
789261.8071620
789591.0327243
789701.0295435
789220.8813412
789760.6932297
789250.5763308

Top tissues by expression

295 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
cortical plateUBERON:000534399.22gold quality
tibiaUBERON:000097998.88gold quality
ganglionic eminenceUBERON:000402398.44gold quality
bronchial epithelial cellCL:000232898.20gold quality
sural nerveUBERON:001548898.10gold quality
epithelium of bronchusUBERON:000203198.01gold quality
bronchusUBERON:000218597.91gold quality
mucosa of paranasal sinusUBERON:000503097.73gold quality
parotid glandUBERON:000183197.64gold quality
embryoUBERON:000092297.24gold quality
mammary ductUBERON:000176596.90gold quality
dorsal motor nucleus of vagus nerveUBERON:000287096.89gold quality
epithelium of mammary glandUBERON:000324496.67gold quality
upper leg skinUBERON:000426296.41gold quality
lateral globus pallidusUBERON:000247695.71gold quality
cartilage tissueUBERON:000241895.67gold quality
trigeminal ganglionUBERON:000167595.40gold quality
skin of hipUBERON:000155495.27gold quality
lateral nuclear group of thalamusUBERON:000273695.07gold quality
renal medullaUBERON:000036294.92gold quality
tracheaUBERON:000312694.83gold quality
calcaneal tendonUBERON:000370194.81gold quality
colonic epitheliumUBERON:000039794.79gold quality
thoracic mammary glandUBERON:000520094.78gold quality
mammary glandUBERON:000191194.76gold quality
saliva-secreting glandUBERON:000104494.71gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451194.62gold quality
lower lobe of lungUBERON:000894994.53gold quality
synovial jointUBERON:000221794.45gold quality
adrenal tissueUBERON:001830394.36gold quality

Single-cell (SCXA)

Detected in 6 experiment(s), a significant marker in 4.

ExperimentMarker?Max mean expression
E-HCAD-5yes58.62
E-MTAB-6678yes24.72
E-CURD-119yes24.15
E-ANND-3yes15.34
E-ANND-2no2101.54
E-MTAB-6379no88.10

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): FOXP2, TBR1

miRNA regulators (miRDB)

186 targeting AUTS2, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4768-5P100.0069.492861
HSA-MIR-6833-3P100.0070.633197
HSA-MIR-6873-3P100.0071.422626
HSA-MIR-5692B100.0071.322622
HSA-MIR-5692C100.0071.322622
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-6867-5P100.0082.213464
HSA-MIR-6740-5P100.0065.64932
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-340-5P100.0072.504437
HSA-MIR-548AW99.9972.573559
HSA-MIR-513B-5P99.9969.962150
HSA-MIR-485-3P99.9870.681585
HSA-MIR-539-3P99.9870.741616
HSA-MIR-548N99.9871.944170
HSA-MIR-548P99.9872.253784
HSA-MIR-1213699.9872.815713
HSA-MIR-520D-5P99.9873.344883
HSA-MIR-524-5P99.9873.434882
HSA-MIR-477599.9875.006394
HSA-MIR-50799.9770.111915
HSA-MIR-60799.9773.625593
HSA-MIR-55799.9670.011640
HSA-MIR-9-3P99.9670.882068
HSA-MIR-365899.9673.874379
HSA-MIR-4666A-3P99.9671.713434

Functional genomics

ClinGen dosage: haploinsufficiency 3 (sufficient evidence), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map

Literature-anchored findings (GeneRIF, showing 38)

  • A de novo balanced translocation breakpoint truncating the autism susceptibility candidate 2 gene is associated with autism. (PMID:20635338)
  • SNP rs6943555 in autism susceptibility candidate 2 gene (AUTS2) was associated with alcohol consumption at genome-wide significance (P = 4 x 10(-8) to P = 4 x 10(-9)). (PMID:21471458)
  • PAX5-AUTS2: a recurrent fusion gene in childhood B-cell precursor acute lymphoblastic leukemia. (PMID:22578776)
  • the role of AUTS2 in normal neurological development and its altered expression may result in a variety of neurobehavioral phenotypes (PMID:22872102)
  • This study indicates that there might be a genetic association of AUTS2 with susceptibility to heroin dependence. Reduced gene expression of AUTS2 in lymphoblastoid cell lines may increase the risk for heroin dependence. (PMID:22995765)
  • These observations demonstrate a causal role of AUTS2 in neurocognitive disorders. (PMID:23332918)
  • our results show that AUTS2 is important for neurodevelopment and expose candidate enhancer sequences in which nucleotide variation could lead to neurological disease and human-specific traits. (PMID:23349641)
  • AUTS2 rs6943555 A allele is associated with suicide committed after drinking ethanol shortly before death. (PMID:23437340)
  • AUTS2, its discovery, expression, association with autism and other neurological and non-neurological traits, implication in human evolution, function, regulation, and genetic pathways, are reviewed. (PMID:24008202)
  • This is one of the smallest de novo intragenic deletions of AUTS2. (PMID:24459036)
  • AUTS2 mutations are associated with autism spectrum disorder. (PMID:24859339)
  • similarities between the phenotypes of 2 male patients with AUTS2 variants support that AUTS2 syndrome is a single gene disorder. (PMID:25205402)
  • polymorphism rs6943555 might elucidate the pathogenesis of schizophrenia and play an important role in its etiology (PMID:25347278)
  • AA homozygotes of rs6943555 were significantly over-represented in the patients with heroin dependence. (PMID:25398668)
  • the CK2 component of PRC1-AUTS2 neutralizes PRC1 repressive activity, whereas AUTS2-mediated recruitment of P300 leads to gene activation. (PMID:25519132)
  • In summary, our results indicate that AUTS2 is a candidate biomarker for defining liver metastasis of pancreatic cancer and directing personalized therapies. (PMID:25962312)
  • The AUTS2 gene has been repeatedly implicated in neurodevelopmental disorders including autism, intellectual disability and developmental delay. (PMID:26348319)
  • Exonic deletions of AUTS2 is associated with developmental delay and intellectual disability. (PMID:26545289)
  • Heterozygous Disruption of Autism susceptibility candidate 2 Causes Impaired Emotional Control and Cognitive Memory (PMID:26717414)
  • Results showed the frequencies of the AUTS2 haplotypes significantly different between them, and the rs6943555 and rs9886351 A-A haplotype was associated with alcohol dependence in a Japanese population. (PMID:26763194)
  • AUTS2 syndrome emerges as a specific ID syndrome with microcephaly. (PMID:27075013)
  • chromatin complexes PRC1/AUTS2 and PRC2 in a gene network in T-ALL regulating early lymphoid differentiation. (PMID:27322685)
  • This clinical report provides the natural history in the eldest patient yet to be reported, and complements the existing evidence suggesting that disruption of the AUTS2 leads to a recently delineated neurodevelopmental phenotype with a wide spectrum, namely “AUTS2 Syndrome.” (PMID:27531620)
  • This study demonstrated that Cocaine-Induced Chromatin Modifications Associate With Increased Expression and Three-Dimensional Looping of Auts2. (PMID:28577753)
  • BCL7A, BRWD3, and AUTS2 demonstrate significantly higher mutation frequencies among AA cases. These genes are all involved in translocations in B-cell malignancies. Moreover, we detected a significant difference in mutation frequency of TP53 and IRF4 with frequencies higher among CA cases. Our study provides rationale for interrogating diverse tumor cohorts to best understand tumor genomics across populations. (PMID:29166413)
  • significant intergenic synergistic effect between rs16879552 (NRG1) and rs7785360 (AUTS2) was identified through cross-validation. (PMID:29377512)
  • These co-occurring hits involved known disease-associated genes such as SETD5, AUTS2, and NRXN1, and were enriched for cellular and developmental processes. Accurate genetic diagnosis of complex disorders will require complete evaluation of the genetic background even after a candidate disease-associated variant is identified (PMID:30190612)
  • The intragenic exon rearrangements (IERs) involved in SOBP (6q21) exon 2 and 3 and AUTS2 (7q11.22) exon 2-4 were the molecular lesions specific to tumors and were frequently detected in non-Hodgkin B cell lymphoma (B-NHL) samples. These IERs constitute novel genetic alterations of B-NHL, which might be associated with tumorigenesis and be useful as genetic biological markers. (PMID:31686349)
  • Effect of AUTS2 gene rs6943555 variant in male patients with schizophrenia in a Turkish population. (PMID:32574757)
  • Whole Exome Sequencing Reveals a Novel AUTS2 In-Frame Deletion in a Boy with Global Developmental Delay, Absent Speech, Dysmorphic Features, and Cerebral Anomalies. (PMID:33562463)
  • Germ cell mosaicism for AUTS2 exon 6 deletion. (PMID:33577136)
  • Attention Deficit Hyperactivity and Autism Spectrum Disorders as the Core Symptoms of AUTS2 Syndrome: Description of Five New Patients and Update of the Frequency of Manifestations and Genotype-Phenotype Correlation. (PMID:34573342)
  • NRF1 association with AUTS2-Polycomb mediates specific gene activation in the brain. (PMID:34637754)
  • Highly diverse phenotypes of mucopolysaccharidosis type IIIB sibling patients: effects of an additional mutation in the AUTS2 gene. (PMID:35525889)
  • Cerebral organoids containing an AUTS2 missense variant model microcephaly. (PMID:35802027)
  • Structural polymorphism driven by a register shift in a CGAG-rich region found in the promoter of the neurodevelopmental regulator AUTS2 gene. (PMID:36864756)
  • Isolated loss of the AUTS2 long isoform, brain-wide or targeted to Calbindin-lineage cells, generates a specific suite of brain, behavioral, and molecular pathologies. (PMID:37816306)
  • AUTS2 disruption causes neuronal differentiation defects in human cerebral organoids through hyperactivation of the WNT/beta-catenin pathway. (PMID:39174599)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_rerioauts2aENSDARG00000056427
mus_musculusAuts2ENSMUSG00000029673
rattus_norvegicusAuts2ENSRNOG00000000885

Paralogs (2): FBRSL1 (ENSG00000112787), FBRS (ENSG00000156860)

Protein

Protein identifiers

Autism susceptibility gene 2 proteinQ8WXX7 (reviewed: Q8WXX7)

All UniProt accessions (18): A0A024RDL5, A0A087WVB5, A0A2R8Y516, A0A2R8Y522, A0A2R8Y568, A0A2R8Y6Q9, A0A2R8Y8C6, A0A2R8YEX6, A0A590UJA2, A0A590UJP3, A0A590UK55, A0A590UKA2, A0A8V8TPM5, Q8WXX7, H7C090, H7C1G5, H7C2P0, Q75MD7

UniProt curated annotations — full annotation on UniProt →

Function. Component of a Polycomb group (PcG) multiprotein PRC1-like complex, a complex class required to maintain the transcriptionally repressive state of many genes, including Hox genes, throughout development. PcG PRC1 complex acts via chromatin remodeling and modification of histones; it mediates monoubiquitination of histone H2A ‘Lys-119’, rendering chromatin heritably changed in its expressibility. The PRC1-like complex that contains PCGF5, RNF2, CSNK2B, RYBP and AUTS2 has decreased histone H2A ubiquitination activity, due to the phosphorylation of RNF2 by CSNK2B. As a consequence, the complex mediates transcriptional activation. In the cytoplasm, plays a role in axon and dendrite elongation and in neuronal migration during embryonic brain development. Promotes reorganization of the actin cytoskeleton, lamellipodia formation and neurite elongation via its interaction with RAC guanine nucleotide exchange factors, which then leads to the activation of RAC1.

Subunit / interactions. Component of a PRC1-like complex that contains PCGF5, RNF2, CSNK2B, RYBP and AUTS2. Within this complex, interacts directly with PCGF5 and CSNK2B. Interacts with the histone acetyltransferase EP300/p300. Interacts (via Pro-rich region) with PREX1, DOCK1 and ELMO2.

Subcellular location. Nucleus. Cytoplasm. Cytoskeleton. Cell projection. Growth cone.

Tissue specificity. Strongly expressed in brain, skeletal muscle and kidney. Also expressed in placenta, lung and leukocytes.

Disease relevance. Intellectual developmental disorder, autosomal dominant 26 (MRD26) [MIM:615834] A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. Additional MRD26 features include autism, short stature, microcephaly, cerebral palsy, and facial dysmorphisms. The disease is caused by variants affecting the gene represented in this entry.

Domain organisation. The Pro-rich region is important for the interaction with RAC guanine nucleotide exchange factors and the subsequent activation of RAC1, which then promotes lamellipodia formation.

Similarity. Belongs to the AUTS2 family.

Isoforms (4)

UniProt IDNamesCanonical?
Q8WXX7-11yes
Q8WXX7-22
Q8WXX7-33
Q8WXX7-55

RefSeq proteins (3): NP_001120703, NP_001120704, NP_056385* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR023246AUTS2Family

Pfam: PF15336

UniProt features (33 total): compositionally biased region 17, region of interest 7, splice variant 4, modified residue 2, chain 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8WXX7-F141.890.00

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (2): 1198, 1233

Function

Pathways and Gene Ontology

Reactome pathways

5 pathways

IDPathway
R-HSA-8939243RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known
R-HSA-212436Generic Transcription Pathway
R-HSA-73857RNA Polymerase II Transcription
R-HSA-74160Gene expression (Transcription)
R-HSA-8878171Transcriptional regulation by RUNX1

MSigDB gene sets: 483 (showing top): BEGUM_TARGETS_OF_PAX3_FOXO1_FUSION_UP, GOBP_NEURON_PROJECTION_EXTENSION, PEREZ_TP63_TARGETS, GCANCTGNY_MYOD_Q6, KAAB_HEART_ATRIUM_VS_VENTRICLE_UP, GOBP_GROWTH, GOBP_REGULATION_OF_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION, GOBP_NEUROGENESIS, CTATGCA_MIR153, BROWNE_HCMV_INFECTION_12HR_UP, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GGGTGGRR_PAX4_03, GOBP_REGULATION_OF_LAMELLIPODIUM_ASSEMBLY, RODWELL_AGING_KIDNEY_NO_BLOOD_DN, AGCGCTT_MIR518F_MIR518E_MIR518A

GO Biological Process (7): neuron migration (GO:0001764), positive regulation of lamellipodium assembly (GO:0010592), actin cytoskeleton organization (GO:0030036), positive regulation of Rac protein signal transduction (GO:0035022), positive regulation of transcription by RNA polymerase II (GO:0045944), axon extension (GO:0048675), dendrite extension (GO:0097484)

GO Molecular Function (2): chromatin binding (GO:0003682), protein binding (GO:0005515)

GO Cellular Component (6): nucleus (GO:0005634), cytoskeleton (GO:0005856), growth cone (GO:0030426), cytoplasm (GO:0005737), actin cytoskeleton (GO:0015629), cell projection (GO:0042995)

Reactome top-level categories

Rollup of top-4 pathways:

CategoryPathways
Transcriptional regulation by RUNX11
RNA Polymerase II Transcription1
Gene expression (Transcription)1
Generic Transcription Pathway1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
neuron projection extension2
binding2
cellular anatomical structure2
cell migration1
generation of neurons1
regulation of lamellipodium assembly1
lamellipodium assembly1
positive regulation of plasma membrane bounded cell projection assembly1
positive regulation of lamellipodium organization1
cytoskeleton organization1
actin filament-based process1
Rac protein signal transduction1
regulation of Rac protein signal transduction1
positive regulation of small GTPase mediated signal transduction1
regulation of transcription by RNA polymerase II1
transcription by RNA polymerase II1
positive regulation of DNA-templated transcription1
axonogenesis1
intracellular membrane-bounded organelle1
intracellular membraneless organelle1
site of polarized growth1
distal axon1
intracellular anatomical structure1
cytoskeleton1

Protein interactions and networks

STRING

1542 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
AUTS2CADPS2Q86UW7871
AUTS2CNTNAP2Q9UHC6828
AUTS2NRG3P56975825
AUTS2PCGF5Q86SE9812
AUTS2DYRK1AQ13627788
AUTS2NRXN1Q9ULB1740
AUTS2PCGF3Q3KNV8736
AUTS2SHANK3Q9BYB0728
AUTS2SHANK2Q9UPX8678
AUTS2CALN1Q9BXU9647
AUTS2NLGN3Q9NZ94645
AUTS2NLGN4XQ8N0W4629
AUTS2YAF2Q8IY57626
AUTS2CHD8Q9HCK8619
AUTS2PCGF1Q9BSM1612

IntAct

59 interactions, top by confidence:

ABTypeScore
CSNK2A1CSNK2A2psi-mi:“MI:0914”(association)0.920
RNF2PCGF5psi-mi:“MI:0914”(association)0.890
PCGF5CSNK2A2psi-mi:“MI:0914”(association)0.880
RYBPBMI1psi-mi:“MI:0914”(association)0.850
CSNK2A1EIF3Jpsi-mi:“MI:0914”(association)0.810
AUTS2PCGF5psi-mi:“MI:0915”(physical association)0.790
AUTS2PCGF5psi-mi:“MI:0914”(association)0.790
PCGF5AUTS2psi-mi:“MI:0914”(association)0.790
CSNK2A2EIF3Jpsi-mi:“MI:0914”(association)0.790
AUTS2CSNK2Bpsi-mi:“MI:0914”(association)0.760
AUTS2RNF2psi-mi:“MI:0915”(physical association)0.740
RYBPE2F6psi-mi:“MI:0914”(association)0.740
DCAF7DIAPH1psi-mi:“MI:0914”(association)0.730
RING1CBX4psi-mi:“MI:0914”(association)0.730
AUTS2EP300psi-mi:“MI:0915”(physical association)0.680
AUTS2EP300psi-mi:“MI:0914”(association)0.680
CSNK2BNMT2psi-mi:“MI:0914”(association)0.660
RNF2CBX4psi-mi:“MI:0914”(association)0.660
PCGF6CBX4psi-mi:“MI:0914”(association)0.640
YAF2E2F6psi-mi:“MI:0914”(association)0.640

BioGRID (99): AUTS2 (Affinity Capture-MS), AUTS2 (Affinity Capture-MS), AUTS2 (Affinity Capture-MS), PCGF5 (Affinity Capture-MS), RING1 (Affinity Capture-MS), RNF2 (Affinity Capture-MS), RYBP (Affinity Capture-MS), YAF2 (Affinity Capture-MS), CSNK2A1 (Affinity Capture-MS), CSNK2A2 (Affinity Capture-MS), CSNK2B (Affinity Capture-MS), DCAF7 (Affinity Capture-MS), FBRS (Affinity Capture-MS), PCGF3 (Affinity Capture-MS), EP300 (Affinity Capture-MS)

ESM2 similar proteins: A0A087WPF7, A0A0R4IBL7, O09000, O54972, O70305, O75081, O75376, P15806, P15881, P15884, P15923, P21677, P30985, P51514, P98180, Q05AQ8, Q14157, Q14687, Q1LY51, Q2VPM4, Q3U3C9, Q4KKX4, Q4VCS5, Q566L4, Q5F3B1, Q5SFM8, Q5T6F2, Q60722, Q60974, Q61286, Q62655, Q6DIH5, Q7ZWN6, Q7ZXS3, Q80X50, Q86YP4, Q8BZ47, Q8CHY6, Q8IXK0, Q8VHG2

Diamond homologs: A0A087WPF7, Q8R089, Q8WXX7, Q9HAH7, Q9HCM7

SIGNOR signaling

8 interactions.

AEffectBMechanism
AUTS2“down-regulates activity”“Polycomb repressive complex 1”binding
AUTS2up-regulatesNeuron_migration
AUTS2up-regulatesNeurite_outgrowth
FOXP2“up-regulates quantity by expression”AUTS2“transcriptional regulation”
AUTS2“up-regulates activity”PREX1binding
AUTS2“up-regulates activity”ELMO2binding
AUTS2“up-regulates activity”DOCK1binding
TBR1“up-regulates quantity by expression”AUTS2“transcriptional regulation”

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 42 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known1194.5×8e-18
Transcriptional Regulation by E2F6758.6×2e-09
SUMOylation of transcription cofactors534.7×1e-05
SUMOylation of RNA binding proteins534.0×1e-05
Differentiation of naive CD4+ T cells to T helper 2 cells (Th2 cells)520.9×9e-05

GO biological processes:

GO termPartnersFoldFDR
negative regulation of proteasomal ubiquitin-dependent protein catabolic process550.1×1e-05
chromatin remodeling610.9×1e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

1416 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic114
Likely pathogenic48
Uncertain significance604
Likely benign359
Benign146

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1033782NM_015570.4(AUTS2):c.2T>C (p.Met1Thr)Pathogenic
1072549NC_000007.13:g.(?70227856)(70242160_?)delPathogenic
1174542NM_015570.4(AUTS2):c.1A>T (p.Met1Leu)Pathogenic
1194595NM_015570.4(AUTS2):c.2392C>T (p.Arg798Ter)Pathogenic
1307520NM_015570.4(AUTS2):c.1610A>C (p.His537Pro)Pathogenic
1310114NM_015570.4(AUTS2):c.1588_1611del (p.Gln530_His537del)Pathogenic
1324010NM_015570.4(AUTS2):c.479_487delinsC (p.Gln160fs)Pathogenic
1325825NM_015570.4:c.(690+1_691-1)_(742+1_743-1)delPathogenic
133343NC_000007.14:g.(69899499_70118132)_(70134571_70435751)delPathogenic
133344NC_000007.14:g.(70435782_70698569)_(70766334_70768023)delPathogenic
1334416NM_015570.4(AUTS2):c.1995_1996del (p.Lys666fs)Pathogenic
1335669NM_015570.4(AUTS2):c.1904_1907dup (p.Pro638fs)Pathogenic
144722GRCh38/hg38 7q11.22(chr7:69865751-70055580)x1Pathogenic
144764GRCh38/hg38 7q11.22(chr7:69000832-70244446)x1Pathogenic
144927GRCh38/hg38 7q11.22(chr7:69828711-70038445)x1Pathogenic
144933GRCh38/hg38 7q11.22(chr7:69588764-69765039)x1Pathogenic
145611GRCh38/hg38 7q11.22(chr7:70792749-72444391)x1Pathogenic
1456517NC_000007.13:g.(?69092299)(70193818_?)delPathogenic
1457603NM_015570.4(AUTS2):c.2008C>T (p.Gln670Ter)Pathogenic
148274GRCh38/hg38 7q11.22(chr7:69665251-70271848)x1Pathogenic
149086GRCh38/hg38 7q11.22(chr7:70206515-70493590)x1Pathogenic
149942GRCh38/hg38 7q11.22(chr7:70724914-70755760)x1Pathogenic
1527360GRCh37/hg19 7q11.22(chr7:69145364-70023881)Pathogenic
1527361GRCh37/hg19 7q11.22(chr7:69250058-71604236)Pathogenic
1527362GRCh37/hg19 7q11.22(chr7:69325515-69644230)Pathogenic
1527363GRCh37/hg19 7q11.22(chr7:69459746-70176827)Pathogenic
1527364GRCh37/hg19 7q11.22(chr7:69527664-69647986)Pathogenic
1527875NM_015570.4(AUTS2):c.1913del (p.Pro638fs)Pathogenic
155372GRCh38/hg38 7q11.22(chr7:70300438-70447453)x1Pathogenic
1708260NM_015570.4(AUTS2):c.2218del (p.His740fs)Pathogenic

SpliceAI

12404 predictions. Top by Δscore:

VariantEffectΔscore
7:69599961:AGGTA:Adonor_loss1.0000
7:69599962:GGT:Gdonor_loss1.0000
7:69599963:GT:Gdonor_loss1.0000
7:69599964:T:Gdonor_loss1.0000
7:69797076:A:AGacceptor_gain1.0000
7:69899282:A:AGacceptor_gain1.0000
7:69899283:C:Gacceptor_gain1.0000
7:69899283:CA:Cacceptor_loss1.0000
7:69899284:A:AGacceptor_gain1.0000
7:69899285:G:GAacceptor_gain1.0000
7:69899285:GA:Gacceptor_gain1.0000
7:69899285:GAA:Gacceptor_gain1.0000
7:69899285:GAAA:Gacceptor_gain1.0000
7:69899494:GACAG:Gdonor_gain1.0000
7:69899495:ACAGG:Adonor_loss1.0000
7:69899496:CAGG:Cdonor_loss1.0000
7:69899497:AGGT:Adonor_loss1.0000
7:69899498:GGTGA:Gdonor_loss1.0000
7:69899499:G:GAdonor_loss1.0000
7:69899500:T:Gdonor_loss1.0000
7:69899504:G:GTdonor_gain1.0000
7:70118127:TTTA:Tacceptor_loss1.0000
7:70118130:A:AGacceptor_gain1.0000
7:70118130:A:Cacceptor_loss1.0000
7:70118131:G:GCacceptor_gain1.0000
7:70118131:GCTC:Gacceptor_gain1.0000
7:70118131:GCTCA:Gacceptor_gain1.0000
7:70118220:A:Tdonor_gain1.0000
7:70118229:GTGAT:Gdonor_gain1.0000
7:70118231:GAT:Gdonor_gain1.0000

AlphaMissense

8244 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
7:69599925:T:CF91S1.000
7:70766138:T:AL498Q1.000
7:70766138:T:CL498P1.000
7:70766149:T:CF502L1.000
7:70766150:T:CF502S1.000
7:70766150:T:GF502C1.000
7:70766151:T:AF502L1.000
7:70766151:T:GF502L1.000
7:70766218:C:GH525D1.000
7:70766224:C:GH527D1.000
7:70766230:C:GH529D1.000
7:70766236:C:GH531D1.000
7:70766248:C:GH535D1.000
7:70766260:C:GH539D1.000
7:70771627:G:AG605R1.000
7:70771627:G:CG605R1.000
7:70771633:T:CF607L1.000
7:70771634:T:CF607S1.000
7:70771634:T:GF607C1.000
7:70771635:T:AF607L1.000
7:70771635:T:GF607L1.000
7:70777109:G:AG647R1.000
7:70777109:G:CG647R1.000
7:70777109:G:TG647W1.000
7:70777110:G:AG647E1.000
7:70777115:T:AW649R1.000
7:70777115:T:CW649R1.000
7:70777116:G:CW649S1.000
7:70777117:G:CW649C1.000
7:70777117:G:TW649C1.000

dbSNP variants (sampled 300 via entrez): RS1000005152 (7:70391221 T>C), RS1000005882 (7:70021596 A>G), RS1000006364 (7:70422229 A>G,T), RS1000010270 (7:69886219 A>G), RS1000011510 (7:70065347 A>G), RS1000011913 (7:70384481 C>T), RS1000013335 (7:69614220 A>G), RS1000019026 (7:70727910 T>C), RS1000021958 (7:69689934 C>G,T), RS1000025245 (7:70208774 A>T), RS1000025887 (7:70505149 T>C), RS1000028332 (7:69742028 T>C), RS1000028409 (7:70108520 A>G), RS1000035434 (7:70297669 C>T), RS1000036076 (7:70765645 C>T)

Disease associations

OMIM: gene MIM:607270 | disease phenotypes: MIM:615834, MIM:209850, MIM:608636, MIM:618050, MIM:213000, MIM:217990

GenCC curated gene-disease

DiseaseClassificationInheritance
syndromic intellectual disabilityDefinitiveAutosomal dominant
autism spectrum disorder due to AUTS2 deficiencyDefinitiveAutosomal dominant

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
syndromic intellectual disabilityDefinitiveAD

Mondo (12): autism spectrum disorder due to AUTS2 deficiency (MONDO:0014361), intellectual disability (MONDO:0001071), multiple congenital anomalies/dysmorphic syndrome-intellectual disability (MONDO:0015159), breast ductal adenocarcinoma (MONDO:0005590), autism spectrum disorder (MONDO:0005258), syndromic intellectual disability (MONDO:0000508), autism (MONDO:0005260), 15q11q13 microduplication syndrome (MONDO:0012081), intellectual disability, autosomal dominant 57 (MONDO:0054837), isolated cerebellar hypoplasia/agenesis (MONDO:0008939), corpus callosum, agenesis of (MONDO:0009022), microcephaly (MONDO:0001149)

Orphanet (9): Autism spectrum disorder due to AUTS2 deficiency (Orphanet:352490), Multiple congenital anomalies/dysmorphic syndrome-intellectual disability (Orphanet:102283), Rare genetic syndromic intellectual disability (Orphanet:183763), 15q11q13 microduplication syndrome (Orphanet:238446), Isolated cerebellar agenesis (Orphanet:1398), Isolated corpus callosum agenesis (Orphanet:200), Cerebellar hypoplasia-tapetoretinal degeneration syndrome (Orphanet:2246), NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658), NON RARE IN EUROPE: Autism (Orphanet:106)

HPO phenotypes

70 total (30 of 70 shown, HPO-id order):

HPOTerm
HP:0000006Autosomal dominant inheritance
HP:0000023Inguinal hernia
HP:0000028Cryptorchidism
HP:0000154Wide mouth
HP:0000160Narrow mouth
HP:0000248Brachycephaly
HP:0000252Microcephaly
HP:0000278Retrognathia
HP:0000286Epicanthus
HP:0000316Hypertelorism
HP:0000322Short philtrum
HP:0000347Micrognathia
HP:0000369Low-set ears
HP:0000431Wide nasal bridge
HP:0000463Anteverted nares
HP:0000486Strabismus
HP:0000494Downslanted palpebral fissures
HP:0000508Ptosis
HP:0000520Proptosis
HP:0000574Thick eyebrow
HP:0000582Upslanted palpebral fissure
HP:0000722Compulsive behaviors
HP:0000729Autistic behavior
HP:0000733Motor stereotypy
HP:0000750Delayed speech and language development
HP:0000752Hyperactivity
HP:0000964Eczematoid dermatitis
HP:0001249Intellectual disability
HP:0001250Seizure
HP:0001257Spasticity

GWAS associations

57 associations (top):

StudyTraitp-value
GCST001029_1Alcohol consumption4.000000e-08
GCST001535_3Immune reponse to smallpox (secreted IL-2)2.000000e-08
GCST001548_4Male-pattern baldness2.000000e-09
GCST001647_5Bipolar disorder5.000000e-06
GCST001762_718Obesity-related traits4.000000e-07
GCST002337_41Amyotrophic lateral sclerosis (sporadic)6.000000e-07
GCST002759_25Motion sickness2.000000e-09
GCST002759_4Motion sickness5.000000e-22
GCST002783_111Body mass index6.000000e-06
GCST003118_1Response to serotonin reuptake inhibitors in non-psychotic unipolar depression2.000000e-08
GCST003901_13Cognitive decline (age-related)3.000000e-06
GCST003983_6Male-pattern baldness2.000000e-26
GCST003991_10Childhood ear infection4.000000e-09
GCST003992_20Photic sneeze reflex1.000000e-08
GCST003996_22Monobrow2.000000e-09
GCST004863_96Mosquito bite size3.000000e-06
GCST004904_36Body mass index4.000000e-12
GCST004904_57Body mass index5.000000e-12
GCST005013_20Childhood ear infection4.000000e-09
GCST005116_7Male-pattern baldness2.000000e-41
GCST005116_8Male-pattern baldness8.000000e-27
GCST005171_49QT interval1.000000e-07
GCST005830_129Hand grip strength9.000000e-10
GCST005830_77Hand grip strength7.000000e-09
GCST006269_716General cognitive ability2.000000e-09
GCST006269_810General cognitive ability8.000000e-09
GCST006630_10Diastolic blood pressure9.000000e-09
GCST006661_171Male-pattern baldness5.000000e-11
GCST006661_318Male-pattern baldness5.000000e-08
GCST006661_319Male-pattern baldness5.000000e-08

EFO canonical traits (27, from GWAS)

EFO IDTrait name
EFO:0004329alcohol drinking
EFO:0004645response to vaccine
EFO:0004873cytokine measurement
EFO:0005108arm span
EFO:0006928motion sickness
EFO:0004340body mass index
EFO:0005658response to selective serotonin reuptake inhibitor
EFO:0007904susceptibility to childhood ear infection measurement
EFO:0007887autosomal dominant compelling helio-ophthalmic outburst syndrome
EFO:0007906synophrys measurement
EFO:0008378mosquito bite reaction size measurement
EFO:0004682QT interval
EFO:0006941grip strength measurement
EFO:0004337intelligence
EFO:0006336diastolic blood pressure
EFO:0009594irritability measurement
EFO:0004763p-tau measurement
EFO:0008579risk-taking behaviour
EFO:0008328chronotype measurement
EFO:0006781coffee consumption measurement
EFO:0007778urinary albumin to creatinine ratio
EFO:0005670smoking initiation
EFO:0600027hemoglobin change measurement
EFO:0004980appendicular lean mass
EFO:0004587lymphocyte count
EFO:0004527mean corpuscular hemoglobin
EFO:0004305erythrocyte count

MeSH disease descriptors (6)

DescriptorNameTree numbers
D061085Agenesis of Corpus CallosumC10.500.034; C16.131.666.034; C23.300.008
D001321Autistic DisorderF03.625.164.113.500
D018270Carcinoma, Ductal, BreastC04.557.470.200.025.232.500; C04.557.470.615.132.500; C04.588.180.390; C17.800.090.500.390
D008607Intellectual DisabilityC10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539
D008831MicrocephalyC05.660.207.620; C10.500.507.400.500; C16.131.621.207.620; C16.131.666.507.400.500
C562568Cerebellar Hypoplasia (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

57 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, decreases expression, increases expression, increases methylation5
Tobacco Smoke Pollutiondecreases expression, increases methylation3
methylmercuric chlorideincreases expression2
bisphenol Aaffects methylation, affects cotreatment, increases methylation, decreases expression2
sodium arseniteaffects methylation, decreases expression2
Benzo(a)pyreneincreases expression, increases methylation2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
Tretinoinincreases expression, decreases expression2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxidedecreases expression2
Cadmium Chloridedecreases expression, increases abundance, increases expression2
aristolochic acid Idecreases expression1
FR900359increases phosphorylation1
trichostatin Adecreases expression1
butyraldehydedecreases expression1
zinc chromatedecreases expression, increases abundance1
tobacco tardecreases expression1
benzo(e)pyreneaffects methylation1
nickel sulfateincreases expression1
beta-methylcholineaffects expression1
di-n-butylphosphoric acidaffects expression1
chromium hexavalent iondecreases expression, increases abundance1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
candoxinincreases expression1
abrinedecreases expression1
dorsomorphinaffects cotreatment, decreases expression1
bisphenol Sdecreases methylation1
jinfukangaffects cotreatment, decreases expression1
Resveratrolaffects cotreatment, decreases expression1
Temozolomideincreases expression1
Arsenic Trioxideincreases expression1

Cellosaurus cell lines

3 cell lines: 3 induced pluripotent stem cell

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_C9JKSDQLCHi060-AInduced pluripotent stem cellMale
CVCL_D4ZVSDQLCHi072-AInduced pluripotent stem cellMale
CVCL_XI75SDQLCHi008-AInduced pluripotent stem cellMale

Clinical trials (associated diseases)

198 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT05657860PHASE4COMPLETEDGuanfacine Extended Release for the Reduction of Aggression and Self-injurious Behavior Associated With Prader-Willi Syndrome
NCT05744479PHASE4RECRUITINGMetformin for Antipsychotic-induced Weight Gain in Adults With Intellectual Disability
NCT06107829PHASE4WITHDRAWNValbenazine Treatment of Tardive Dyskinesia in Adults With Intellectual/Developmental Disabilities
NCT06997198PHASE4NOT_YET_RECRUITINGDeutetrabenazine Treatment for Tardive Dyskinesia in Intellectual/Developmental Disabilities
NCT02270736PHASE3COMPLETEDClinical Study to Investigate the Efficacy and Safety of NT 201 Compared to Placebo in the Treatment of Chronic Troublesome Drooling Associated With Neurological Disorders and/or Intellectual Disability
NCT02304302PHASE2COMPLETEDDown Syndrome Memantine Follow-up Study
NCT03862950PHASE2COMPLETEDA Trial of Metformin in Individuals With Fragile X Syndrome (Met)
NCT04529226PHASE2UNKNOWNStudy to Compare Clozapine vs Treatment as Usual in People With Intellectual Disability & Treatment-resistant Psychosis
NCT04821856PHASE2COMPLETEDEvaluation of the Effectiveness of Cannabidiol in Treating Severe Behavioural Problems in Children and Adolescents With Intellectual Disability
NCT05273320PHASE1COMPLETEDClinical Trial of Nabilone for Aggression in Adults With Intellectual and Developmental Disabilities
NCT05301361PHASE1ENROLLING_BY_INVITATIONSensitivity of the NIH Toolbox to Stimulant Treatment in Intellectual Disabilities
NCT06016764PHASE1COMPLETEDUse of MRI and cTBS for Catatonia in Autism
NCT06586827PHASE1COMPLETEDImpact of Competency-Based Training and Technical Assistance Employment Outcomes of Individuals With ID/DD
NCT07531940PHASE1NOT_YET_RECRUITINGEscalating Doses of Memantine in Down Syndrome (MEDS-123)
NCT01238250Not specifiedRECRUITINGOnline Study of People Who Have Genetic Changes and Features of Autism: Simons Searchlight
NCT03479476PHASE2/PHASE3COMPLETEDA Trial of Metformin in Individuals With Fragile X Syndrome
NCT02616796PHASE1/PHASE2COMPLETEDEffects of Social Gaze Training on Brain and Behavior in Fragile X Syndrome
NCT06860672EARLY_PHASE1RECRUITINGClinical Trial of the Dual Vector Base Editor for the Treatment of the CHD3-R1025W Mutation
NCT00597948Not specifiedCOMPLETEDHealthy Lifestyles for People With Intellectual Disabilities
NCT01087320Not specifiedRECRUITINGGenome Medical Sequencing for Gene Discovery
NCT01652963Not specifiedUNKNOWNPicture-based Computerised Assessment and Training of Cognitive Behaviour Therapy Skills
NCT01695395Not specifiedCOMPLETEDMental Health Care Provision for Adults With Intellectual Disability and a Mental Disorder
NCT01867554Not specifiedCOMPLETEDResearch and Characterization of New Genes Involved in Intellectual Disability
NCT01915381Not specifiedCOMPLETEDImproving Adherence Healthy Lifestyle With a Smartphone Application Based on Adults With Intellectual Disabilities
NCT01988623Not specifiedCOMPLETEDPivotal Response Treatment for Individuals With Intellectual Disabilities
NCT02099773Not specifiedCOMPLETEDSupport Staff-client Interactions With Augmentative and Alternative Communication
NCT02136849Not specifiedCOMPLETEDInter-regional Project of the Great Western Exploration Approach for Exome Molecular Causes Severe Intellectual Disability Isolated or Syndromic
NCT02225041Not specifiedCOMPLETEDSedation Strategy and Cognitive Outcome After Critical Illness in Early Childhood
NCT02414438Not specifiedCOMPLETEDEstablishing the Clinical Utility of First StepDx PLUS and NextStepDx PLUS Study
NCT02451761Not specifiedCOMPLETEDApparently Balanced Chromosomal Translocation/ Next-generation Sequencing/ Intellectual Disability
NCT02461420Not specifiedACTIVE_NOT_RECRUITINGMapping the Genotype, Phenotype, and Natural History of Phelan-McDermid Syndrome
NCT02461459Not specifiedACTIVE_NOT_RECRUITINGAutism Spectrum Disorder (ASD) and Intellectual Disability (ID) Determinants in Tuberous Sclerosis Complex (TSC)
NCT02486081Not specifiedCOMPLETEDDevelopment and Application-Smart Football for Movement Evaluation and Training in the Special Education Population
NCT02504502Not specifiedCOMPLETEDEnhancing Genomic Laboratory Reports to Enhance Communication and Empower Patients
NCT02513277Not specifiedCOMPLETEDDiabetes Screening & Prevention for People With Learning (Intellectual) Disabilities:STOP Diabetes Study
NCT02561754Not specifiedCOMPLETEDWeight Management for Adolescents With IDD
NCT02591446Not specifiedCOMPLETEDTranscranial Magnetic Stimulation Studies in Autism Spectrum Disorders
NCT02714868Not specifiedCOMPLETEDEvaluation of Project TEAM (Teens Making Environmental and Activity Modifications)
NCT02721394Not specifiedUNKNOWNFCT With Young Children With ID in the UK: A Feasibility Project V.1
NCT02746614Not specifiedCOMPLETEDPsychomotor Therapy Effects in Adaptive Behavior and Motor Proficiency in Intellectual Disability