DNAAF4 dynein axonemal assembly factor 4 [Homo sapiens (human)] - Gene

Summary

Official Symbol: DNAAF4provided by HGNC
Official Full Name: dynein axonemal assembly factor 4provided by HGNC
Primary source: HGNC:HGNC:21493
See related: Ensembl:ENSG00000256061 MIM:608706; AllianceGenome:HGNC:21493
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: RD; DYX1; EKN1; pf23; DYXC1; CILD25; DYX1C1
Summary: This gene encodes a tetratricopeptide repeat domain-containing protein. The encoded protein interacts with estrogen receptors and the heat shock proteins, Hsp70 and Hsp90. An homologous protein in rat has been shown to function in neuronal migration in the developing neocortex. A chromosomal translocation involving this gene is associated with a susceptibility to developmental dyslexia. Mutations in this gene are associated with deficits in reading and spelling. Alternative splicing results in multiple transcript variants. Read-through transcription also exists between this gene and the downstream cell cycle progression 1 (CCPG1) gene. [provided by RefSeq, Mar 2011]
Expression: Broad expression in testis (RPKM 4.6), thyroid (RPKM 3.5) and 15 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 15q21.3

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	15	NC_000015.10 (55417755..55508234, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	15	NC_060939.1 (53220992..53311451, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	15	NC_000015.9 (55709953..55800432, complement)

Chromosome 15 - NC_000015.10 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?

As a first exploitation of this unique cohort, we identify three novel candidate dyslexia genes, ZNF280D and TCF12 at 15q21, and PDE7B at 6q23.3, by molecular mapping of the familial translocation with the 15q21 breakpoint.
Title: A cohort of balanced reciprocal translocations associated with dyslexia: identification of two putative candidate genes at DYX1.
Developmental dyslexia susceptibility genes DNAAF4, DCDC2, and NRSN1 are associated with brain function in fluently reading adolescents and young adults.
Title: Developmental dyslexia susceptibility genes DNAAF4, DCDC2, and NRSN1 are associated with brain function in fluently reading adolescents and young adults.
A novel homozygous splice variant in DNAAF4 is associated with asthenozoospermia.
Title: A novel homozygous splice variant in DNAAF4 is associated with asthenozoospermia.
Novel dynein axonemal assembly factor 1 mutations identified using wholeexome sequencing in patients with primary ciliary dyskinesia.
Title: Novel dynein axonemal assembly factor 1 mutations identified using whole‑exome sequencing in patients with primary ciliary dyskinesia.
that endogenous DYX1C1 localizes to the base of the cilium, whereas DCDC2 localizes along the entire axoneme of the cilium
Title: Ciliary dyslexia candidate genes DYX1C1 and DCDC2 are regulated by Regulatory Factor X (RFX) transcription factors through X-box promoter motifs.
promoter SNP rs12899331 of DYX1C1 may contribute towards the manifestation of DD. This study supports the association of DYX1C1 with DD in an Indian population
Title: Association of SNPs of DYX1C1 with developmental dyslexia in an Indian population.
results demonstrate that DYX1C1 can modulate the expression of genes involved in cell migration and nervous system development and associates with a number of cytoskeletal proteins.
Title: Molecular networks of DYX1C1 gene show connection to neuronal migration genes and cytoskeletal proteins.
DYX1C1 is required for axonemal dynein assembly and ciliary motility.
Title: DYX1C1 is required for axonemal dynein assembly and ciliary motility.
The results of this study do not provide evidence for association between the putatively functional single nucleotide polymorphisms -3G/A and 1249G/T in DYX1C1 and reading disabilities.
Title: A family-based association analysis and meta-analysis of the reading disabilities candidate gene DYX1C1.
Gene-by-environment effects were found between some specified environmental moderators (i.e. maternal smoke during pregnancy, birth weight and socio-economic status) and the DYX1C1-1259C/G marker
Title: An assessment of gene-by-environment interactions in developmental dyslexia-related phenotypes.

Submit: New GeneRIF Correction See all GeneRIFs (35)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Dyslexia, susceptibility to, 1 MedGen: C1851967 OMIM: 127700 GeneReviews: Not available	Compare labs
Primary ciliary dyskinesia 25 MedGen: C3809641 OMIM: 615482 GeneReviews: Primary Ciliary Dyskinesia	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

RH92020 (e-PCR)
- UniSTS:91203

G62640 (e-PCR)
- UniSTS:139620

G60057 (e-PCR)
- UniSTS:137319

D15S994 (e-PCR)
- UniSTS:23656

D15S1049 (e-PCR), detects polymorphism
- UniSTS:24951

RH64680 (e-PCR)
- UniSTS:87936

D15S146 (e-PCR), detects polymorphism
- UniSTS:51370

RH94002 (e-PCR)
- UniSTS:88513

SHGC-149990 (e-PCR)
- UniSTS:177353

D15S143 (e-PCR), detects polymorphism
- UniSTS:35538

G54607 (e-PCR)
- UniSTS:117742

D15S132 (e-PCR)
- UniSTS:38129

Readthrough DNAAF4-CCPG1

Readthrough gene: DNAAF4-CCPG1, Included gene: CCPG1

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables nuclear estrogen receptor binding	IBA Inferred from Biological aspect of Ancestor more info
enables nuclear estrogen receptor binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in cilium movement	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in determination of left/right symmetry	IBA Inferred from Biological aspect of Ancestor more info
involved_in determination of left/right symmetry	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in epithelial cilium movement involved in extracellular fluid movement	IBA Inferred from Biological aspect of Ancestor more info
involved_in establishment of localization in cell	IEA Inferred from Electronic Annotation more info
involved_in heart development	IBA Inferred from Biological aspect of Ancestor more info
involved_in inner dynein arm assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in inner dynein arm assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in learning or memory	IEA Inferred from Electronic Annotation more info
involved_in neuron migration	ISS Inferred from Sequence or Structural Similarity more info
involved_in outer dynein arm assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in outer dynein arm assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of intracellular estrogen receptor signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of proteasomal protein catabolic process	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in centrosome	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info
located_in dynein axonemal particle	ISS Inferred from Sequence or Structural Similarity more info
located_in extracellular region	IEA Inferred from Electronic Annotation more info
located_in neuron projection	IEA Inferred from Electronic Annotation more info
located_in non-motile cilium	IEA Inferred from Electronic Annotation more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in plasma membrane	IDA Inferred from Direct Assay more info

General protein information

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Preferred Names: dynein axonemal assembly factor 4

Names: dynein assembly factor 4, axonemal; dyslexia susceptibility 1 candidate 1; dyslexia susceptibility 1 candidate gene 1 protein

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_021213.1 RefSeqGene

Range

5001..82927

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001033559.3 → NP_001028731.1 dynein axonemal assembly factor 4 isoform b

See identical proteins and their annotated locations for NP_001028731.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate exon that causes a frameshift in the 3' coding region, compared to variant 1. The encoded isoform (b) has a distinct and shorter C-terminus, compared to isoform a.

Source sequence(s)

AF337549, AK095201, BC017392

Consensus CDS

CCDS32244.1

UniProtKB/Swiss-Prot

Q8WXU2

Related

ENSP00000402640.2, ENST00000457155.6

Conserved Domains (3) summary

cd06469
Location:10 → 87

p23_DYX1C1_like; p23_like domain found in proteins similar to dyslexia susceptibility 1 (DYX1) candidate 1 (C1) protein, DYX1C1. The human gene encoding this protein is a positional candidate gene for developmental dyslexia (DD), it is located on 15q21.3 by the DYX1 DD ...

sd00006
Location:290 → 318

TPR; TPR repeat [structural motif]

pfam13414
Location:289 → 353

TPR_11; TPR repeat
NM_001033560.2 → NP_001028732.1 dynein axonemal assembly factor 4 isoform c

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (c) has a distinct and shorter C-terminus, compared to isoform a.

Source sequence(s)

AF337549, AK095201, BC062564, BM971229

Consensus CDS

CCDS32243.1

UniProtKB/TrEMBL

A0A0S2Z5Z4

Related

ENSP00000403412.2, ENST00000448430.6

Conserved Domains (3) summary

cd06469
Location:10 → 87

p23_DYX1C1_like; p23_like domain found in proteins similar to dyslexia susceptibility 1 (DYX1) candidate 1 (C1) protein, DYX1C1. The human gene encoding this protein is a positional candidate gene for developmental dyslexia (DD), it is located on 15q21.3 by the DYX1 DD ...

sd00006
Location:290 → 318

TPR; TPR repeat [structural motif]

pfam13414
Location:289 → 349

TPR_11; TPR repeat
NM_130810.4 → NP_570722.2 dynein axonemal assembly factor 4 isoform a

See identical proteins and their annotated locations for NP_570722.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).

Source sequence(s)

AF337549, AK095201, BC017392

Consensus CDS

CCDS10154.1

UniProtKB/Swiss-Prot

Q6P5Y9, Q8N1S6, Q8WXU2

Related

ENSP00000323275.3, ENST00000321149.7

Conserved Domains (4) summary

cd06469
Location:10 → 87

p23_DYX1C1_like; p23_like domain found in proteins similar to dyslexia susceptibility 1 (DYX1) candidate 1 (C1) protein, DYX1C1. The human gene encoding this protein is a positional candidate gene for developmental dyslexia (DD), it is located on 15q21.3 by the DYX1 DD ...

sd00006
Location:290 → 318

TPR; TPR repeat [structural motif]

pfam00515
Location:367 → 399

TPR_1; Tetratricopeptide repeat

pfam13414
Location:289 → 353

TPR_11; TPR repeat