DEAF1 DEAF1 transcription factor [Homo sapiens (human)] - Gene

Summary

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: mouse all
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Genomic context

Location:: 11p15.5

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (644220..707083, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (694847..758083, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (644220..707083, complement)

Chromosome 11 - NC_000011.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

Project title: HPA RNA-seq normal tissues 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Transcriptional Regulation of the Human 5-HT1A Receptor Gene by Lithium: Role of Deaf1 and GSK3beta.
Title: Transcriptional Regulation of the Human 5-HT1A Receptor Gene by Lithium: Role of Deaf1 and GSK3β.
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.
this study shows that Deaf1 promotes eccrine gland formation
Title: The Transcription Factor Deaf1 Modulates Engrailed-1 Expression to Regulate Skin Appendage Fate.
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.
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.
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.
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.
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.
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.
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].

Submit: New GeneRIF Correction See all GeneRIFs (25)

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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

STS-D51166 (e-PCR)
- UniSTS:22616

RH12540 (e-PCR)
- UniSTS:56674

D11S2273E (e-PCR)
- UniSTS:63600

SHGC-31847 (e-PCR)
- UniSTS:25262

G62137 (e-PCR)
- UniSTS:139205

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
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
involved_in transcription by RNA polymerase II	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in chromatin	ISA Inferred from Sequence Alignment more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
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
located_in nucleus	IDA Inferred from Direct Assay 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

NG_034156.2 RefSeqGene

Range

16862..67851

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
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, Q59EI0

Related

ENSP00000507198.1, ENST00000683307.1
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

A8K1F8, A8K5R8, C7T5V5, O15152, O75398, O75399, O75510, O75511, O75512, O75513, Q9UET1

UniProtKB/TrEMBL

A0A8I5KZ80

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_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000011.10 Reference GRCh38.p14 Primary Assembly

Range

644220..707083 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

A0A804HIS1

Related

ENST00000528864.6
XM_047426249.1 → XP_047282205.1 deformed epidermal autoregulatory factor 1 homolog isoform X3

Related

ENSP00000510621.1, ENST00000689835.1
XM_047426248.1 → XP_047282204.1 deformed epidermal autoregulatory factor 1 homolog isoform X1
XM_011519842.4 → XP_011518144.1 deformed epidermal autoregulatory factor 1 homolog isoform X2

UniProtKB/TrEMBL

A0A8I5KZ80

Conserved Domains (2) summary

pfam01342
Location:198 → 272

SAND; SAND domain

pfam01753
Location:504 → 531

zf-MYND; MYND finger
XM_047426250.1 → XP_047282206.1 deformed epidermal autoregulatory factor 1 homolog isoform X4

RNA

XR_007062436.1 RNA Sequence
XR_007062437.1 RNA Sequence

Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

NT_187586.1 Reference GRCh38.p14 ALT_REF_LOCI_1

Range

176100..206711 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

NC_060935.1 Alternate T2T-CHM13v2.0

Range

694847..758083 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

UniProtKB/TrEMBL

A0A804HIS1
XM_054367464.1 → XP_054223439.1 deformed epidermal autoregulatory factor 1 homolog isoform X3
XM_054367462.1 → XP_054223437.1 deformed epidermal autoregulatory factor 1 homolog isoform X1
XM_054367463.1 → XP_054223438.1 deformed epidermal autoregulatory factor 1 homolog isoform X2
XM_054367465.1 → XP_054223440.1 deformed epidermal autoregulatory factor 1 homolog isoform X4