This gene encodes a large protein whose specific function is unknown. Absence of the orthologous protein in mouse results in embryonic lethality with deficient axial rotation, abnormal differentiation of the neural tube, and randomized looping of the heart tube during development. In human, mutations in this gene are associated with polymicrogyria with seizures. In human fibrob... See more...

Aliases for RTTN Gene

Aliases for RTTN Gene

  • Rotatin 2 3 4 5
  • DKFZP434G145 2
  • MSSP 3
  • RTTN 5

External Ids for RTTN Gene

Previous GeneCards Identifiers for RTTN Gene

  • GC18M067493
  • GC18M067730
  • GC18M065820
  • GC18M065822
  • GC18M064389

Summaries for RTTN Gene

Entrez Gene Summary for RTTN Gene

  • This gene encodes a large protein whose specific function is unknown. Absence of the orthologous protein in mouse results in embryonic lethality with deficient axial rotation, abnormal differentiation of the neural tube, and randomized looping of the heart tube during development. In human, mutations in this gene are associated with polymicrogyria with seizures. In human fibroblasts this protein localizes at the ciliary basal bodies. Given the intracellular localization of this protein and the phenotypic effects of mutations, this gene is suspected of playing a role in the maintenance of normal ciliary structure which in turn effects the developmental process of left-right organ specification, axial rotation, and perhaps notochord development. [provided by RefSeq, Jan 2013]

GeneCards Summary for RTTN Gene

RTTN (Rotatin) is a Protein Coding gene. Diseases associated with RTTN include Microcephaly, Short Stature, And Polymicrogyria With Or Without Seizures and Polymicrogyria. Gene Ontology (GO) annotations related to this gene include binding.

UniProtKB/Swiss-Prot Summary for RTTN Gene

  • Involved in the genetic cascade that governs left-right specification. Plays a role in the maintenance of a normal ciliary structure. Required for correct asymmetric expression of NODAL, LEFTY and PITX2.

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for RTTN Gene

Genomics for RTTN Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for RTTN Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH18J070204 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE CraniofacialAtlas 261.3 -0.1 -74 2.8 BCLAF1 SP1 ZNF654 ZNF207 IKZF1 ZNF600 SIX5 ZNF580 KLF9 POLR2A RTTN ENSG00000287646 LOC105372180 SOCS6 HSALNG0122276
GH18J069400 Promoter/Enhancer 2 EPDnew FANTOM5 Ensembl ENCODE CraniofacialAtlas 10.2 +804.4 804425 3.4 KLF9 POLR2A YY1 ZFP64 HOMEZ SIN3A KMT2B THAP11 FOXA2 SMAD4 DOK6 HSALNG0122249 RTTN RF00994-448 CD226
GH18J070375 Promoter/Enhancer 1.8 EPDnew Ensembl ENCODE dbSUPER 11.1 -175.3 -175318 11.2 NCOR1 IKZF1 SSRP1 CEBPA NFIC CHD4 YY1 REST CEBPB HOMEZ LINC01910 SOCS6 RTTN piR-50437-317 HSALNG0122284 LIVAR
GH18J070418 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 11.3 -216.5 -216482 8.4 JUND CEBPA ATF3 YY1 MXD4 CEBPB FEZF1 HOMEZ MAX EP300 SOCS6 RTTN LARP7P3 CD226 HSALNG0122289 HSALNG0122292 LINC01910
GH18J070294 Promoter/Enhancer 1.4 Ensembl ENCODE dbSUPER 10.5 -90.3 -90310 2.8 IKZF1 SSRP1 CEBPA KLF11 MNT HOMEZ KMT2B THAP11 SMAD4 RXRA RTTN LINC01909 SOCS6 RF00017-2431
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RTTN on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RTTN

Top Transcription factor binding sites by QIAGEN in the RTTN gene promoter:
  • AML1a
  • AREB6
  • C/EBPalpha
  • E47
  • FOXO1
  • FOXO1a
  • NF-kappaB
  • NF-kappaB1
  • POU2F1
  • POU2F1a

Genomic Locations for RTTN Gene

Latest Assembly
chr18:70,003,031-70,205,726
(GRCh38/hg38)
Size:
202,696 bases
Orientation:
Minus strand

Previous Assembly
chr18:67,670,267-67,872,923
(GRCh37/hg19 by Entrez Gene)
Size:
202,657 bases
Orientation:
Minus strand

chr18:67,671,029-67,873,181
(GRCh37/hg19 by Ensembl)
Size:
202,153 bases
Orientation:
Minus strand

Genomic View for RTTN Gene

Genes around RTTN on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RTTN Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RTTN Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RTTN Gene

Proteins for RTTN Gene

  • Protein details for RTTN Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q86VV8-RTTN_HUMAN
    Recommended name:
    Rotatin
    Protein Accession:
    Q86VV8
    Secondary Accessions:
    • Q68CS9
    • Q6ZRL8
    • Q6ZTK3
    • Q86TG4
    • Q8N8N8
    • Q8TBQ4
    • Q96IN9
    • Q9UFJ4

    Protein attributes for RTTN Gene

    Size:
    2226 amino acids
    Molecular mass:
    248630 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=BAC86583.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=BAC87292.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305}; Sequence=BAC87292.1; Type=Miscellaneous discrepancy; Note=Aberrant splicing.; Evidence={ECO:0000305}; Sequence=CAH18659.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000305};
    Miscellaneous:
    • [Isoform 2]: May be due to an intron retention.
    • [Isoform 4]: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

    Alternative splice isoforms for RTTN Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for RTTN Gene

Post-translational modifications for RTTN Gene

  • Ubiquitination at Lys1528
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for RTTN Gene

Domains & Families for RTTN Gene

Gene Families for RTTN Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Predicted intracellular proteins

Protein Domains for RTTN Gene

Suggested Antigen Peptide Sequences for RTTN Gene

GenScript: Design optimal peptide antigens:
  • Rotatin (RTTN_HUMAN)
genes like me logo Genes that share domains with RTTN: view

No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for RTTN Gene

Function for RTTN Gene

Molecular function for RTTN Gene

UniProtKB/Swiss-Prot Function:
Involved in the genetic cascade that governs left-right specification. Plays a role in the maintenance of a normal ciliary structure. Required for correct asymmetric expression of NODAL, LEFTY and PITX2.

Phenotypes From GWAS Catalog for RTTN Gene

genes like me logo Genes that share phenotypes with RTTN: view

Human Phenotype Ontology for RTTN Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

miRNA for RTTN Gene

miRTarBase miRNAs that target RTTN

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RTTN

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Animal Models , Transcription Factor Targets and HOMER Transcription for RTTN Gene

Localization for RTTN Gene

Subcellular locations from UniProtKB/Swiss-Prot for RTTN Gene

Cytoplasm, cytoskeleton, cilium basal body. Cytoplasm, cytoskeleton, microtubule organizing center, centrosome. Note=Colocalizes with the basal bodies at the primary cilium.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RTTN gene
Compartment Confidence
cytoskeleton 5
plasma membrane 3
mitochondrion 2
extracellular 1
nucleus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Centrosome (3)
  • Cytosol (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for RTTN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005813 centrosome IEA --
GO:0005814 centriole IBA 21873635
GO:0005815 microtubule organizing center IEA --
GO:0005856 cytoskeleton IEA --
genes like me logo Genes that share ontologies with RTTN: view

Pathways & Interactions for RTTN Gene

PathCards logo

SuperPathways for RTTN Gene

No Data Available

Gene Ontology (GO) - Biological Process for RTTN Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007099 centriole replication IBA 21873635
GO:0007275 multicellular organism development IEA --
GO:0007368 determination of left/right symmetry IEA --
GO:0010457 centriole-centriole cohesion IBA 21873635
GO:0032053 ciliary basal body organization IBA 21873635
genes like me logo Genes that share ontologies with RTTN: view

No data available for Pathways by source and SIGNOR curated interactions for RTTN Gene

Drugs & Compounds for RTTN Gene

No Compound Related Data Available

Transcripts for RTTN Gene

mRNA/cDNA for RTTN Gene

2 REFSEQ mRNAs :
15 NCBI additional mRNA sequence :
25 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

Inhibitory RNAs for research

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for RTTN

Alternative Splicing Database (ASD) splice patterns (SP) for RTTN Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13a · 13b ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^ 21 ^ 22 ^ 23 ^ 24 ^
SP1: -
SP2:
SP3:
SP4:
SP5:

ExUns: 25 ^ 26 ^ 27 ^ 28 ^ 29 ^ 30 ^ 31 ^ 32 ^ 33 ^ 34 ^ 35 ^ 36 ^ 37 ^ 38 ^ 39 ^ 40 ^ 41 ^ 42 ^ 43a · 43b ^ 44 ^ 45a · 45b ^ 46 ^ 47a · 47b ^
SP1: - -
SP2:
SP3: -
SP4:
SP5: -

ExUns: 48 ^ 49 ^ 50a · 50b · 50c
SP1:
SP2:
SP3:
SP4: -
SP5:

Relevant External Links for RTTN Gene

GeneLoc Exon Structure for
RTTN

Expression for RTTN Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for RTTN Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for RTTN Gene



Protein tissue co-expression partners for RTTN Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RTTN

SOURCE GeneReport for Unigene cluster for RTTN Gene:

Hs.654809

Evidence on tissue expression from TISSUES for RTTN Gene

  • Nervous system(4.5)
  • Blood(4.2)
  • Kidney(4.1)
  • Pancreas(4)

Phenotype-based relationships between genes and organs from Gene ORGANizer for RTTN Gene

Germ Layers:
  • ectoderm
Systems:
  • nervous
  • skeleton
Regions:
Head and neck:
  • brain
  • cerebellum
  • head
  • skull
genes like me logo Genes that share expression patterns with RTTN: view

Primer products for research

No data available for mRNA differential expression in normal tissues , Protein differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for RTTN Gene

Orthologs for RTTN Gene

This gene was present in the common ancestor of chordates.

Orthologs for RTTN Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia RTTN 29 30
  • 99.1 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia RTTN 29 30
  • 87.62 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Rttn 29 16 30
  • 83.88 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia RTTN 29 30
  • 83.76 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Rttn 29
  • 83.39 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 30
  • 76 (a)
OneToMany
-- 30
  • 69 (a)
OneToMany
-- 30
  • 57 (a)
OneToMany
-- 30
  • 55 (a)
OneToMany
Oppossum
(Monodelphis domestica)
Mammalia RTTN 30
  • 65 (a)
OneToOne
Chicken
(Gallus gallus)
Aves RTTN 29 30
  • 69.45 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia RTTN 30
  • 64 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia rttn 29
  • 61.53 (n)
Zebrafish
(Danio rerio)
Actinopterygii rttn 29 30
  • 55.72 (n)
OneToOne
Sea Squirt
(Ciona savignyi)
Ascidiacea -- 30
  • 26 (a)
OneToOne
Species where no ortholog for RTTN was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for RTTN Gene

ENSEMBL:
Gene Tree for RTTN (if available)
TreeFam:
Gene Tree for RTTN (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RTTN: view image
Alliance of Genome Resources:
Additional Orthologs for RTTN

Paralogs for RTTN Gene

No data available for Paralogs for RTTN Gene

Variants for RTTN Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RTTN Gene

SNP ID Clinical significance and condition Chr 18 pos Variation AA Info Type
1012914 Uncertain Significance: not provided 70,149,007(-) T/C
NM_173630.4(RTTN):c.2203A>G (p.Asn735Asp)
MISSENSE_VARIANT,FIVE_PRIME_UTR
1031271 Pathogenic: Microcephaly, short stature, and polymicrogyria with or without seizures 70,139,660(-) AC/A
NM_173630.4(RTTN):c.2726del (p.Gly909fs)
FRAMESHIFT_VARIANT,FIVE_PRIME_UTR
1031272 Uncertain Significance: Microcephaly, short stature, and polymicrogyria with or without seizures 70,204,133(-) G/A
NM_173630.4(RTTN):c.350C>T (p.Ser117Leu)
MISSENSE_VARIANT,FIVE_PRIME_UTR
1031273 Uncertain Significance: Microcephaly, short stature, and polymicrogyria with or without seizures 70,092,680(-) C/T
NM_173630.4(RTTN):c.4028G>A (p.Ser1343Asn)
MISSENSE
1031274 Uncertain Significance: Microcephaly, short stature, and polymicrogyria with or without seizures 70,075,473(-) T/A
NM_173630.4(RTTN):c.4443A>T (p.Leu1481Phe)
MISSENSE

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for RTTN Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for RTTN Gene

Variant ID Type Subtype PubMed ID
esv32736 CNV gain+loss 17666407
esv3396488 CNV insertion 20981092
esv3583135 CNV loss 25503493
esv3642981 CNV loss 21293372
nsv1113934 CNV deletion 24896259
nsv510465 OTHER sequence alteration 20534489
nsv577546 CNV loss 21841781
nsv833686 CNV gain 17160897

Variation tolerance for RTTN Gene

Residual Variation Intolerance Score: 5.17% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.65; 72.74% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RTTN Gene

Human Gene Mutation Database (HGMD)
RTTN
SNPedia medical, phenotypic, and genealogical associations of SNPs for
RTTN
Leiden Open Variation Database (LOVD)
RTTN

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RTTN Gene

Disorders for RTTN Gene

MalaCards: The human disease database

(24) MalaCards diseases for RTTN Gene - From: OMI, CVR, GTR, ORP, SWI, COP, and GCD

UniProtKB/Swiss-Prot

RTTN_HUMAN
  • Microcephaly, short stature, and polymicrogyria with or without seizures (MSSP) [MIM:614833]: A disease characterized by many irregular small gyri in the brain surface and fusion of the molecular layer over multiple small gyri, which gives a festooned appearance to the cortical surface, without abnormal neuronal migration. Polymicrogyria is a heterogeneous disorder, considered to be the result of postmigratory abnormal cortical organization. MSSP patients have moderate to severe mental retardation, poor speech, dysarthria and seizures. {ECO:0000269 PubMed:22939636}. Note=The disease is caused by variants affecting the gene represented in this entry.

Additional Disease Information for RTTN

genes like me logo Genes that share disorders with RTTN: view

No data available for Genatlas for RTTN Gene

Publications for RTTN Gene

  1. RTTN mutations link primary cilia function to organization of the human cerebral cortex. (PMID: 22939636) Kheradmand Kia S … Mancini GM (American journal of human genetics 2012) 3 4 72
  2. RTTN Mutations Cause Primary Microcephaly and Primordial Dwarfism in Humans. (PMID: 26608784) Shamseldin H … Alkuraya FS (American journal of human genetics 2015) 3 72
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4
  4. Rotatin is a novel gene required for axial rotation and left-right specification in mouse embryos. (PMID: 11900971) Faisst AM … Gruss P (Mechanisms of development 2002) 2 3
  5. Primary microcephaly, primordial dwarfism, and brachydactyly in adult cases with biallelic skipping of RTTN exon 42. (PMID: 30927481) Zakaria M … Dahl N (Human mutation 2019) 3

Products for RTTN Gene

Sources for RTTN Gene