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DEAF1 DEAF1 transcription factor [ Homo sapiens (human) ]

Gene ID: 10522, updated on 17-May-2023

Summary

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Official Symbol
DEAF1provided by HGNC
Official Full Name
DEAF1 transcription factorprovided by HGNC
Primary source
HGNC:HGNC:14677
See related
Ensembl:ENSG00000177030 MIM:602635; AllianceGenome:HGNC:14677
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SPN; NUDR; VSVS; MRD24; ZMYND5; NEDHELS
Summary
This gene encodes a zinc finger domain-containing protein that functions as a regulator of transcription. The encoded proteins binds to its own promoter as well as to that of several target genes. Activity of this protein is important in the regulation of embryonic development. Mutations in this gene have been found in individuals with autosomal dominant cognitive disability. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2014]
Expression
Ubiquitous expression in brain (RPKM 14.6), thyroid (RPKM 8.8) and 25 other tissues See more
Orthologs
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Genomic context

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See DEAF1 in Genome Data Viewer
Location:
11p15.5
Exon count:
19
Annotation release Status Assembly Chr Location
RS_2023_03 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (644220..707083, complement)
RS_2023_03 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (694847..758083, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (644220..707083, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:640805-641416 Neighboring gene Sharpr-MPRA regulatory region 3787 Neighboring gene uncharacterized LOC124902603 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr11:673917-675116 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:676679-677178 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:679106-679606 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:686586-687086 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:687087-687587 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:688565-689488 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:694659-695198 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:695199-695740 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:695741-696280 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:696821-697360 Neighboring gene transmembrane protein 80 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:704144-705071 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:706927-707853 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:707854-708781 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:709709-710636 Neighboring gene EPS8 like 2

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. De novo variants of DEAF1 cause intellectual disability in six Chinese patients. Chen S, et al. Clin Chim Acta, 2021 Jul. PMID 33705764
  2. De novo and biallelic DEAF1 variants cause a phenotypic spectrum. Nabais Sá MJ, et al. Genet Med, 2019 Sep. PMID 30923367
  3. Functional analysis of novel DEAF1 variants identified through clinical exome sequencing expands DEAF1-associated neurodevelopmental disorder (DAND) phenotype. Chen L, et al. Hum Mutat, 2017 Dec. PMID 28940898, Free PMC Article
  4. Identification of a syndrome comprising microcephaly and intellectual disability but not white matter disease associated with a homozygous c.676C>T p.R226W DEAF1 mutation. Gund C, et al. Am J Med Genet A, 2016 May. PMID 26834045
  5. [Screening of deformed epidermal autoregulatory factor 1-related functional proteins]. Wu X, et al. Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi, 2015 Aug. PMID 26271982

See all (55) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. De novo variants of DEAF1 cause intellectual disability in six Chinese patients.
    Title: De novo variants of DEAF1 cause intellectual disability in six Chinese patients.
  2. this study shows that Deaf1 promotes eccrine gland formation
    Title: The Transcription Factor Deaf1 Modulates Engrailed-1 Expression to Regulate Skin Appendage Fate.
  3. We propose that different variants in the DEAF1 gene result in a phenotypic spectrum centered around neurodevelopmental delay. While a pathogenic de novo dominant variant would also incapacitate the product of the wild-type allele and result in a dominant-negative effect, a combination of two recessive variants would result in a partial loss of function.
    Title: De novo and biallelic DEAF1 variants cause a phenotypic spectrum.
  4. The results demonstrate that variants located within the neurodevelopmental disorder (DAND)or NLS domains significantly reduce DEAF1 transcriptional regulatory activities and are thus, likely to contribute to the underlying clinical concerns in DAND patients.
    Title: Functional analysis of novel DEAF1 variants identified through clinical exome sequencing expands DEAF1-associated neurodevelopmental disorder (DAND) phenotype.
  5. identified pathogenic de novo variants in two cases, a nonsense variant in IQSEC2 and a missense variant in the SAND domain of DEAF1
    Title: Exome analysis of Smith-Magenis-like syndrome cohort identifies de novo likely pathogenic variants.
  6. We conclude that this DEAF1 gene alteration caused this patient's symptoms and that white matter disease should not be considered a obligate feature of this syndrome.
    Title: Identification of a syndrome comprising microcephaly and intellectual disability but not white matter disease associated with a homozygous c.676C>T p.R226W DEAF1 mutation.
  7. RAI1 polymorphisms rs4925102 and rs9907986 are predicted to disrupt the binding of retinoic acid RXR-RAR receptors and the transcription factor DEAF1, respectively, in Smith-Magenis and Potocki-Lupski syndromes patients.
    Title: Evidence for genetic regulation of mRNA expression of the dosage-sensitive gene retinoic acid induced-1 (RAI1) in human brain.
  8. an autosomal recessive splice acceptor mutation in DEAF1 (c.997+4A>C, p.G292Pfs*) in all affected individuals, which led to exon skipping, and reduced the normal full-length mRNA copy number in the patients with epilepsy and extrapyramidal symptoms
    Title: Recessive DEAF1 mutation associates with autism, intellectual disability, basal ganglia dysfunction and epilepsy.
  9. Data show that deformed epidermal autoregulatory factor-1 (DEAF1) was located in the nucleus under the fluorescence microscope.
    Title: [Screening of deformed epidermal autoregulatory factor 1-related functional proteins].
  10. These data suggest that during the progression of type 1 diabetes, inflammation and hyperglycemia mediate the splicing of DEAF1 and loss of peripheral tissue antigen expression.
    Title: Inflammation and hyperglycemia mediate Deaf1 splicing in the pancreatic lymph nodes via distinct pathways during type 1 diabetes.
Submit: New GeneRIF Correction See all GeneRIFs (24)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Intellectual disability, autosomal dominant 24
MedGen: C4014414 OMIM: 615828 GeneReviews: Not available
Compare labs
Intellectual disability-epilepsy-extrapyramidal syndrome
MedGen: C4310683 OMIM: 617171 GeneReviews: Not available
Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription factor activity, RNA polymerase II-specific IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
enables DNA-binding transcription factor activity, RNA polymerase II-specific ISA
Inferred from Sequence Alignment
more info
  
enables DNA-binding transcription repressor activity, RNA polymerase II-specific IDA
Inferred from Direct Assay
more info
 PubMed 
enables RNA polymerase II transcription regulatory region sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in anatomical structure morphogenesis TAS
Traceable Author Statement
more info
 PubMed 
involved_in embryonic skeletal system development ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in germ cell development TAS
Traceable Author Statement
more info
 PubMed 
involved_in negative regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in negative regulation of transcription by RNA polymerase II IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in neural tube closure ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in positive regulation of DNA-templated transcription IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of mammary gland epithelial cell proliferation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
involved_in transcription by RNA polymerase II TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
part_of chromatin ISA
Inferred from Sequence Alignment
more info
  
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
located_in extracellular region IEA
Inferred from Electronic Annotation
more info
  
located_in fibrillar center IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 

General protein information

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Preferred Names
deformed epidermal autoregulatory factor 1 homolog
Names
nuclear DEAF-1-related transcriptional regulator
suppressin
zinc finger MYND domain-containing protein 5

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_034156.2 RefSeqGene

    Range
    16862..67851
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001293634.1 → NP_001280563.1  deformed epidermal autoregulatory factor 1 homolog isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2, also known as DF1-VAR) lacks two internal coding exons and contains an alternate coding exon, compared to variant 1. The encoded isoform (b) is shorter than isoform a.
    Source sequence(s)
    AC131934, AK291383, BC053322, FJ985253, HY094363, HY324291
    UniProtKB/Swiss-Prot
    O75398
    Conserved Domains (2) summary
    pfam01753
    Location:429 → 465
    zf-MYND; MYND finger
    cl02536
    Location:198 → 222
    SAND; SAND domain

  2. NM_001367390.1 → NP_001354319.1  deformed epidermal autoregulatory factor 1 homolog isoform c

    Status: REVIEWED

    Source sequence(s)
    AC131934, AP006284, AP006621
    Consensus CDS
    CCDS91398.1
    UniProtKB/TrEMBL
    A0A804HIS1
    Related
    ENSP00000507198.1, ENST00000683307.1

  3. NM_021008.4 → NP_066288.2  deformed epidermal autoregulatory factor 1 homolog isoform a

    See identical proteins and their annotated locations for NP_066288.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
    Source sequence(s)
    AK291383, AP006284
    Consensus CDS
    CCDS31327.1
    UniProtKB/Swiss-Prot
    O75398, Q9UET1
    Related
    ENSP00000371846.3, ENST00000382409.4
    Conserved Domains (2) summary
    pfam01342
    Location:200 → 272
    SAND; SAND domain
    pfam01753
    Location:504 → 540
    zf-MYND; MYND finger

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_03

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p14 Primary Assembly

    Range
    644220..707083 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047426251.1 → XP_047282207.1  deformed epidermal autoregulatory factor 1 homolog isoform X5

    UniProtKB/TrEMBL
    A0A804HIS1
    Related
    ENST00000528864.6

  2. XM_047426249.1 → XP_047282205.1  deformed epidermal autoregulatory factor 1 homolog isoform X3

    Related
    ENSP00000510621.1, ENST00000689835.1

  3. XM_047426248.1 → XP_047282204.1  deformed epidermal autoregulatory factor 1 homolog isoform X1

  4. XM_011519842.4 → XP_011518144.1  deformed epidermal autoregulatory factor 1 homolog isoform X2

    Conserved Domains (2) summary
    pfam01342
    Location:198 → 272
    SAND; SAND domain
    pfam01753
    Location:504 → 531
    zf-MYND; MYND finger

  5. XM_047426250.1 → XP_047282206.1  deformed epidermal autoregulatory factor 1 homolog isoform X4

RNA

  1. XR_007062436.1 RNA Sequence

  2. XR_007062437.1 RNA Sequence

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NT_187586.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    176100..206711 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060935.1 Alternate T2T-CHM13v2.0

    Range
    694847..758083 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054367466.1 → XP_054223441.1  deformed epidermal autoregulatory factor 1 homolog isoform X5

    UniProtKB/TrEMBL
    A0A804HIS1

  2. XM_054367464.1 → XP_054223439.1  deformed epidermal autoregulatory factor 1 homolog isoform X3

  3. XM_054367462.1 → XP_054223437.1  deformed epidermal autoregulatory factor 1 homolog isoform X1

  4. XM_054367463.1 → XP_054223438.1  deformed epidermal autoregulatory factor 1 homolog isoform X2

  5. XM_054367465.1 → XP_054223440.1  deformed epidermal autoregulatory factor 1 homolog isoform X4

RNA

  1. XR_008488326.1 RNA Sequence

  2. XR_008488327.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O75398.1 GenPept UniProtKB/Swiss-Prot:O75398

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