SPECC1L Gene (Protein Coding)

Sperm Antigen With Calponin Homology And Coiled-Coil Domains 1 Like

GC22P024837
GIFtS:
37
This gene encodes a coiled-coil domain containing protein. The encoded protein may play a critical role in actin-cytoskeletal reorganization during facial morphogenesis. Mutations in this gene are a cause of oblique facial clefting-1. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. A read-through transcript composed of SPEC... See more...

Aliases for SPECC1L Gene

Aliases for SPECC1L Gene

  • Sperm Antigen With Calponin Homology And Coiled-Coil Domains 1 Like 2 3 5
  • Cytokinesis And Spindle Organization A 2 3
  • Renal Carcinoma Antigen NY-REN-22 3 4
  • SPECC1-Like Protein 3 4
  • Cytospin-A 3 4
  • KIAA0376 2 4
  • CYTSA 3 4
  • Sperm Antigen With Calponin Homology And Coiled-Coil Domains 1-Like 4
  • SPECC1-Like 2
  • Cytospin A 2
  • SPECC1L 5
  • OBLFC1 3
  • GBBB2 3
  • TBHS 3

External Ids for SPECC1L Gene

Previous HGNC Symbols for SPECC1L Gene

  • CYTSA

Previous GeneCards Identifiers for SPECC1L Gene

  • GC22P022996
  • GC22P007616
  • GC22P024668
  • GC22P024682
  • GC22P024692
  • GC22P024708
  • GC22P024731
  • GC22P024272
  • GC22P024297
  • GC22P024422
  • GC22P024430
  • GC22P024425
  • GC22P024468
  • GC22P024314
  • GC22P024329
  • GC22P024341
  • GC22P024365
  • GC22P024387
  • GC22P024393
  • GC22P024403
  • GC22P024414

Summaries for SPECC1L Gene

Entrez Gene Summary for SPECC1L Gene

  • This gene encodes a coiled-coil domain containing protein. The encoded protein may play a critical role in actin-cytoskeletal reorganization during facial morphogenesis. Mutations in this gene are a cause of oblique facial clefting-1. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. A read-through transcript composed of SPECC1L (sperm antigen with calponin homology and coiled-coil domains 1-like) and the downstream ADORA2A (adenosine A2a receptor) gene sequence has been identified, but it is thought to be non-coding. [provided by RefSeq, Jun 2013]

GeneCards Summary for SPECC1L Gene

SPECC1L (Sperm Antigen With Calponin Homology And Coiled-Coil Domains 1 Like) is a Protein Coding gene. Diseases associated with SPECC1L include Opitz Gbbb Syndrome, Type Ii and Facial Clefting, Oblique, 1. Gene Ontology (GO) annotations related to this gene include protein dimerization activity. An important paralog of this gene is SPECC1L-ADORA2A.

UniProtKB/Swiss-Prot Summary for SPECC1L Gene

  • Involved in cytokinesis and spindle organization. May play a role in actin cytoskeleton organization and microtubule stabilization and hence required for proper cell adhesion and migration.

Additional gene information for SPECC1L Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SPECC1L Gene

Genomics for SPECC1L Gene

GeneHancer (GH) Regulatory Elements Pubs

Download GeneHancer 2017 data
Promoters and enhancers for SPECC1L Gene
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SPECC1L on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SPECC1L

Genomic Locations for SPECC1L Gene

Genomic Locations for SPECC1L Gene
chr22:24,270,817-24,417,740
(GRCh38/hg38)
Size:
146,924 bases
Orientation:
Plus strand
chr22:24,666,786-24,813,708
(GRCh37/hg19)
Size:
146,923 bases
Orientation:
Plus strand

Genomic View for SPECC1L Gene

Genes around SPECC1L on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SPECC1L Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SPECC1L Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for SPECC1L Gene

Proteins for SPECC1L Gene

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  • Protein details for SPECC1L Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q69YQ0-CYTSA_HUMAN
    Recommended name:
    Cytospin-A
    Protein Accession:
    Q69YQ0
    Secondary Accessions:
    • B7Z758
    • F5H1H6
    • O15081

    Protein attributes for SPECC1L Gene

    Size:
    1117 amino acids
    Molecular mass:
    124602 Da
    Quaternary structure:
    • May interact with both microtubules and actin cytoskeleton.

    Alternative splice isoforms for SPECC1L Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for SPECC1L Gene

Protein Expression for SPECC1L Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for SPECC1L Gene

  • Ubiquitination at Lys382, Lys846, Lys896, Lys904, Lys939, and Lys999
  • Modification sites at PhosphoSitePlus

Other Protein References for SPECC1L Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for SPECC1L Gene

Domains & Families for SPECC1L Gene

Gene Families for SPECC1L Gene

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

Protein Domains for SPECC1L Gene

InterPro:
Blocks:
  • Calponin-like actin-binding
  • 2-oxo acid dehydrogenase, acyltransferase component, lipoyl-binding
ProtoNet:

Suggested Antigen Peptide Sequences for SPECC1L Gene

GenScript: Design optimal peptide antigens:
  • KIAA0376 protein, isoform CRA_a (B2RMV2_HUMAN)
  • cDNA FLJ61179, highly similar to Adenosine A2a receptor (B4DW87_HUMAN)
  • Sperm antigen with calponin homology and coiled-coil domains 1-like (CYTSA_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q69YQ0

UniProtKB/Swiss-Prot:

CYTSA_HUMAN :
  • Belongs to the cytospin-A family.
Family:
  • Belongs to the cytospin-A family.
genes like me logo Genes that share domains with SPECC1L: view

Function for SPECC1L Gene

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Molecular function for SPECC1L Gene

UniProtKB/Swiss-Prot Function:
Involved in cytokinesis and spindle organization. May play a role in actin cytoskeleton organization and microtubule stabilization and hence required for proper cell adhesion and migration.

Phenotypes From GWAS Catalog for SPECC1L Gene

Gene Ontology (GO) - Molecular Function for SPECC1L Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IEA --
genes like me logo Genes that share ontologies with SPECC1L: view
genes like me logo Genes that share phenotypes with SPECC1L: view

Human Phenotype Ontology for SPECC1L Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SPECC1L

Clone Products

No data available for Enzyme Numbers (IUBMB) , Animal Models , Transcription Factor Targets and HOMER Transcription for SPECC1L Gene

Localization for SPECC1L Gene

Subcellular locations from UniProtKB/Swiss-Prot for SPECC1L Gene

Cytoplasm, cytoskeleton. Cytoplasm, cytoskeleton, spindle. Cell junction, gap junction. Note=Colocalizes with acetylated alpha-tubulin, gamma-tubulin and F-actin. Also observed in a ring around gamma-tubulin containing centrioles possibly in the microtubule organizing center.

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 SPECC1L gene
Compartment Confidence
cytoskeleton 4
cytosol 4
plasma membrane 1
extracellular 1
nucleus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Actin filaments (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SPECC1L Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005737 cytoplasm IEA --
GO:0005815 microtubule organizing center IBA 21873635
GO:0005819 spindle IEA --
GO:0005829 cytosol IDA --
GO:0005856 cytoskeleton IEA --
genes like me logo Genes that share ontologies with SPECC1L: view

Pathways & Interactions for SPECC1L Gene

PathCards logo

SuperPathways for SPECC1L Gene

No Data Available

Gene Ontology (GO) - Biological Process for SPECC1L Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0007049 cell cycle IEA --
GO:0007155 cell adhesion IDA 21703590
GO:0030036 actin cytoskeleton organization IBA 21873635
GO:0051301 cell division IEA --
genes like me logo Genes that share ontologies with SPECC1L: view

No data available for Pathways by source and SIGNOR curated interactions for SPECC1L Gene

Drugs & Compounds for SPECC1L Gene

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  1. Drug

(1) Drugs for SPECC1L Gene - From: PharmGKB

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
Methotrexate Approved Pharma Folate antagonist,inhibits DFHR 1825
genes like me logo Genes that share compounds with SPECC1L: view

Transcripts for SPECC1L Gene

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  1. CRISPR
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mRNA/cDNA for SPECC1L Gene

4 REFSEQ mRNAs :
20 NCBI additional mRNA sequence :
8 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SPECC1L

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for SPECC1L Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4 ^ 5 ^ 6a · 6b · 6c ^ 7a · 7b ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13 ^ 14a · 14b ^ 15 ^ 16 ^ 17 ^ 18a · 18b ^ 19a ·
SP1: - -
SP2: - -
SP3: -
SP4:
SP5:
SP6:

ExUns: 19b
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:

Relevant External Links for SPECC1L Gene

GeneLoc Exon Structure for
SPECC1L

Expression for SPECC1L Gene

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  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SPECC1L Gene

mRNA expression in normal human tissues for SPECC1L Gene
mRNA expression by BioGPS for SPECC1L Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for SPECC1L Gene

This gene is overexpressed in Bone marrow stromal cell (20.3), Adrenal (13.2), and Cervix (12.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for SPECC1L Gene



Protein tissue co-expression partners for SPECC1L Gene

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SPECC1L

SOURCE GeneReport for Unigene cluster for SPECC1L Gene:

Hs.474384

Evidence on tissue expression from TISSUES for SPECC1L Gene

  • Nervous system(4.8)
  • Liver(4.4)

Phenotype-based relationships between genes and organs from Gene ORGANizer for SPECC1L Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • cardiovascular
  • digestive
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Regions:
Head and neck:
  • brain
  • cerebellum
  • cheek
  • chin
  • cranial nerve
  • ear
  • epiglottis
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • larynx
  • lip
  • mandible
  • maxilla
  • middle ear
  • mouth
  • neck
  • nose
  • outer ear
  • pharynx
  • scalp
  • skull
  • tongue
  • vocal cord
Thorax:
  • aorta
  • bronchus
  • diaphragm
  • esophagus
  • heart
  • heart valve
  • lung
  • trachea
Abdomen:
  • abdominal wall
  • gallbladder
  • intestine
  • kidney
  • large intestine
  • stomach
Pelvis:
  • anus
  • penis
  • rectum
  • testicle
  • ureter
  • urethra
Limb:
  • digit
  • finger
  • foot
  • hand
  • lower limb
  • toe
  • upper limb
General:
  • blood
  • blood vessel
  • hair
  • peripheral nervous system
  • skin
genes like me logo Genes that share expression patterns with SPECC1L: view

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for SPECC1L Gene

Orthologs for SPECC1L Gene

This gene was present in the common ancestor of animals.

Orthologs for SPECC1L Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
 Mammalia SPECC1L 30 31
  • 99.79 (n)
 OneToOne
Platypus
(Ornithorhynchus anatinus)
 Mammalia -- 31
  • 96 (a)
 OneToMany
Cow
(Bos Taurus)
 Mammalia -- 31
  • 93 (a)
 OneToMany
SPECC1L 30
  • 82.72 (n)
Dog
(Canis familiaris)
 Mammalia SPECC1L 30 31
  • 92.03 (n)
 OneToMany
Mouse
(Mus musculus)
 Mammalia Specc1l 30 17 31
  • 88.42 (n)
 OneToMany
Rat
(Rattus norvegicus)
 Mammalia Specc1l 30
  • 87.32 (n)
Oppossum
(Monodelphis domestica)
 Mammalia -- 31
  • 66 (a)
 OneToMany
Chicken
(Gallus gallus)
 Aves SPECC1L 30 31
  • 80.42 (n)
 OneToMany
Lizard
(Anolis carolinensis)
 Reptilia -- 31
  • 62 (a)
 OneToMany
Tropical Clawed Frog
(Silurana tropicalis)
 Amphibia specc1l 30
  • 69.38 (n)
Zebrafish
(Danio rerio)
 Actinopterygii specc1la 30 31
  • 67.09 (n)
 ManyToMany
specc1lb 31
  • 65 (a)
 ManyToMany
Fruit Fly
(Drosophila melanogaster)
 Insecta CG13366 31
  • 29 (a)
 OneToMany
Sea Squirt
(Ciona savignyi)
 Ascidiacea CSA.3677 31
  • 32 (a)
 OneToMany
Sea Vase
(Ciona intestinalis)
 Ascidiacea Cin.3747 30
Species where no ortholog for SPECC1L 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)
  • 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 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 SPECC1L Gene

ENSEMBL:
Gene Tree for SPECC1L (if available)
TreeFam:
Gene Tree for SPECC1L (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SPECC1L: view image

Paralogs for SPECC1L Gene

Paralogs for SPECC1L Gene

(3) SIMAP similar genes for SPECC1L Gene using alignment to 3 proteins:

  • CYTSA_HUMAN
  • C9J8U1_HUMAN
  • C9JLY8_HUMAN
genes like me logo Genes that share paralogs with SPECC1L: view

Variants for SPECC1L Gene

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Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SPECC1L Gene

SNP ID Clinical significance and condition Chr 22 pos Variation AA Info Type
599382 Likely Pathogenic: Hypertelorism, Teebi type 24,322,229(+) A/C MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT
691567 Uncertain Significance: Craniosynostosis 24,322,895(+) C/T NONSENSE,NON_CODING_TRANSCRIPT_VARIANT
691915 Uncertain Significance: Craniosynostosis 24,322,599(+) G/A MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT
708016 Benign: not provided 24,322,709(+) A/C MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT
708645 Benign: not provided 24,328,848(+) A/G MISSENSE_VARIANT,NON_CODING_TRANSCRIPT_VARIANT

Additional dbSNP identifiers (rs#s) for SPECC1L Gene

Structural Variations from Database of Genomic Variants (DGV) for SPECC1L Gene

Variant ID Type Subtype PubMed ID
dgv4528n100 CNV gain 25217958
dgv8039n54 CNV gain 21841781
esv24290 CNV gain 19812545
esv2724041 CNV deletion 23290073
esv2724068 CNV deletion 23290073
esv3575443 CNV gain 25503493
esv3893463 CNV gain 25118596
esv996036 CNV deletion 20482838
nsv1055830 CNV gain 25217958
nsv1057819 CNV gain 25217958
nsv1110863 OTHER inversion 24896259
nsv526567 CNV gain 19592680
nsv588744 CNV gain 21841781
nsv7350 OTHER inversion 18451855
nsv834158 CNV gain 17160897
nsv834160 CNV gain 17160897
nsv953060 CNV duplication 24416366
nsv953061 CNV deletion 24416366
nsv964609 CNV duplication 23825009
nsv964610 CNV duplication 23825009
nsv966093 CNV duplication 23825009
nsv979658 CNV duplication 23825009
nsv9883 CNV gain+loss 18304495
nsv9884 CNV gain+loss 18304495

Variation tolerance for SPECC1L Gene

Residual Variation Intolerance Score: 17.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.67; 57.00% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SPECC1L Gene

Human Gene Mutation Database (HGMD)
SPECC1L
SNPedia medical, phenotypic, and genealogical associations of SNPs for
SPECC1L

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SPECC1L Gene

Disorders for SPECC1L Gene

MalaCards: The human disease database

(18) MalaCards diseases for SPECC1L Gene - From: UniProtKB/Swiss-Prot, OMIM, ClinVar, GTR, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
opitz gbbb syndrome, type ii
  • gbbb2
facial clefting, oblique, 1
  • oblfc1
hypertelorism, teebi type
  • tbhs
oculomaxillofacial dysostosis
  • oculomaxillofacial dysplasia with oblique facial clefts
macrostomia, isolated
  • lateral cleft, isolated
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

CYTSA_HUMAN
  • Facial clefting, oblique, 1 (OBLFC1) [MIM:600251]: A rare form of facial clefting. A facial cleft is any of the fissures between the embryonic prominences that normally unite to form the face. {ECO:0000269 PubMed:21703590}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Opitz GBBB syndrome 2 (GBBB2) [MIM:145410]: A form of Opitz GBBB syndrome, a congenital midline malformation syndrome characterized by hypertelorism, genital-urinary defects such as hypospadias in males and splayed labia in females, cleft lip/palate, laryngotracheoesophageal abnormalities, imperforate anus, developmental delay and congenital heart defects. {ECO:0000269 PubMed:25412741}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Hypertelorism, Teebi type (TBHS) [MIM:145420]: An autosomal dominant syndrome characterized by an abnormally increased distance between ocular orbits, and facial features that can resemble craniofrontonasal dysplasia such as prominent forehead, widow's peak, heavy and broad eyebrows, long palpebral fissures, ptosis, high and broad nasal bridge, short nose, low-set ears, natal teeth, thin upper lip and a grooved chin. Affected individuals have limb, urogenital, umbilical and cardiac defects. {ECO:0000269 PubMed:26111080}. Note=The disease may be caused by mutations affecting the gene represented in this entry.

Additional Disease Information for SPECC1L

ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with SPECC1L: view

No data available for Genatlas for SPECC1L Gene

Publications for SPECC1L Gene

  1. Prediction of the coding sequences of unidentified human genes. VII. The complete sequences of 100 new cDNA clones from brain which can code for large proteins in vitro. (PMID: 9205841) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 1997) 2 3 4
  2. Expanding the SPECC1L mutation phenotypic spectrum to include Teebi hypertelorism syndrome. (PMID: 26111080) Bhoj EJ … Zackai EH (American journal of medical genetics. Part A 2015) 3 4
  3. Mutations in SPECC1L, encoding sperm antigen with calponin homology and coiled-coil domains 1-like, are found in some cases of autosomal dominant Opitz G/BBB syndrome. (PMID: 25412741) Kruszka P … Zackai EH (Journal of medical genetics 2015) 3 4
  4. Deficiency of the cytoskeletal protein SPECC1L leads to oblique facial clefting. (PMID: 21703590) Saadi I … Maas RL (American journal of human genetics 2011) 3 4
  5. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4

ExternalLinks

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