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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
  • CYTSA 3 4
  • Sperm Antigen With Calponin Homology And Coiled-Coil Domains 1-Like 4
  • SPECC1-Like 2
  • Cytospin-A 3
  • Cytospin A 2
  • KIAA0376 4
  • OBLFC1 3
  • GBBB2 3

External Ids for SPECC1L Gene

Previous HGNC Symbols for SPECC1L Gene


Previous GeneCards Identifiers for SPECC1L Gene

  • GC22P022996
  • GC22P007616
  • GC22P024668
  • GC22P024682
  • GC22P024692
  • GC22P024708
  • GC22P024731
  • GC22P024272
  • GC22P024297
  • GC22P024314
  • GC22P024329
  • GC22P024341
  • GC22P024365
  • GC22P024387
  • GC22P024393

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 Facial Clefting, Oblique, 1 and Opitz Gbbb Syndrome, Type Ii. Gene Ontology (GO) annotations related to this gene include protein dimerization activity. An important paralog of this gene is SPECC1L-ADORA2A.

UniProtKB/Swiss-Prot 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 , fRNAdb sequence ontologies and piRNA Summary for SPECC1L Gene

Genomics for SPECC1L Gene

GeneHancer (GH) Regulatory Elements for SPECC1L Gene

Promoters and enhancers for SPECC1L Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH22J024270 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 675.1 +0.6 644 2.5 HDGF FOXA2 ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2 POLR2B ZNF213 SPECC1L SPECC1L-ADORA2A RPS10P29 POM121L9P SMARCB1 GGTLC4P ENSG00000272578 ZNF70 CABIN1 LOC105372960
GH22J024302 Promoter/Enhancer 1.5 EPDnew Ensembl ENCODE 661.6 +33.2 33234 3.9 FOXA2 NFIB ZSCAN4 NEUROD1 SIN3A FEZF1 RAD21 RFX5 RARA YY1 SPECC1L POM121L9P UPB1 ENSG00000228923 ADORA2A BCRP3 SPECC1L-ADORA2A LOC105372960
GH22J024323 Promoter 0.9 EPDnew 650.2 +53.2 53171 0.1 ATF2 YY1 NFIL3 SP1 HNF1A JUND ATF3 HNF4A ATF7 SPECC1L SPECC1L-ADORA2A LOC105372960
GH22J024411 Promoter 0.5 EPDnew 650.1 +140.6 140590 0.1 SPECC1L ADORA2A-AS1 UPB1 LOC105372960 ADORA2A SPECC1L-ADORA2A
GH22J024632 Enhancer 1.1 Ensembl ENCODE 72.5 +362.3 362284 1.4 HDGF ARNT GLI4 TCF12 ZNF121 ARID2 ZNF207 ZNF662 ZNF488 MEF2D ENSG00000284233 BCRP3 SPECC1L ENSG00000272977 ZNF70 ENSG00000272578 SMARCB1 ENSG00000232545 CABIN1 GGT1
- 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 UCSC Golden Path with GeneCards custom track

Genomic Locations for SPECC1L Gene

Genomic Locations for SPECC1L Gene
146,924 bases
Plus strand
146,923 bases
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 StructureGene Density

RefSeq DNA sequence for SPECC1L Gene

Proteins for SPECC1L Gene

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

    Protein Symbol:
    Recommended name:
    Protein Accession:
    Secondary Accessions:
    • B7Z758
    • F5H1H6
    • O15081

    Protein attributes for SPECC1L Gene

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

    Alternative splice isoforms for SPECC1L Gene


neXtProt entry for SPECC1L Gene

Post-translational modifications for SPECC1L Gene

  • Ubiquitination at posLast=999999, posLast=939939, isoforms=2904, and isoforms=2846
  • Modification sites at PhosphoSitePlus

Other Protein References for SPECC1L Gene

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

Graphical View of Domain Structure for InterPro Entry



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

Function for SPECC1L Gene

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

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

Clone Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , 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

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

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 --
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

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 --
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

(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 1603
genes like me logo Genes that share compounds with SPECC1L: view

Transcripts for SPECC1L Gene

mRNA/cDNA for SPECC1L Gene

Unigene Clusters for SPECC1L Gene

Sperm antigen with calponin homology and coiled-coil domains 1-like:
Representative Sequences:

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: -

ExUns: 19b

Relevant External Links for SPECC1L Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for SPECC1L Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE 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

NURSA nuclear receptor signaling pathways regulating expression of SPECC1L Gene:


SOURCE GeneReport for Unigene cluster for SPECC1L Gene:


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
  • cardiovascular
  • digestive
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
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
  • aorta
  • bronchus
  • diaphragm
  • esophagus
  • heart
  • heart valve
  • lung
  • trachea
  • abdominal wall
  • gallbladder
  • intestine
  • kidney
  • large intestine
  • stomach
  • anus
  • penis
  • rectum
  • testicle
  • ureter
  • urethra
  • digit
  • finger
  • foot
  • hand
  • lower limb
  • toe
  • upper limb
  • 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
(Pan troglodytes)
Mammalia SPECC1L 34 33
  • 99.79 (n)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 96 (a)
(Bos Taurus)
Mammalia -- 34
  • 93 (a)
  • 82.72 (n)
(Canis familiaris)
Mammalia SPECC1L 34 33
  • 92.03 (n)
(Mus musculus)
Mammalia Specc1l 16 34 33
  • 88.42 (n)
(Rattus norvegicus)
Mammalia Specc1l 33
  • 87.32 (n)
(Monodelphis domestica)
Mammalia -- 34
  • 66 (a)
(Gallus gallus)
Aves SPECC1L 34 33
  • 80.42 (n)
(Anolis carolinensis)
Reptilia -- 34
  • 62 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia specc1l 33
  • 69.38 (n)
(Danio rerio)
Actinopterygii specc1la 34 33
  • 67.09 (n)
specc1lb 34
  • 65 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG13366 34
  • 29 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.3677 34
  • 32 (a)
Cin.3747 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.3747 33
Species where no ortholog for SPECC1L was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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

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

Paralogs for SPECC1L Gene

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

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

Variants for SPECC1L Gene

Sequence variations from dbSNP and Humsavar for SPECC1L Gene

SNP ID Clin Chr 22 pos Variation AA Info Type
rs193920978 uncertain-significance, Malignant tumor of prostate 24,321,444(+) G/A/T coding_sequence_variant, genic_upstream_transcript_variant, missense_variant
rs387907108 pathogenic, Oculomaxillofacial dysostosis 24,322,224(+) A/C coding_sequence_variant, genic_upstream_transcript_variant, missense_variant
rs786201030 pathogenic, Opitz G/BBB syndrome 24,322,169(+) A/C coding_sequence_variant, genic_upstream_transcript_variant, missense_variant
rs786201031 pathogenic, Opitz G/BBB syndrome 24,412,690(+) G/A coding_sequence_variant, missense_variant
VAR_066873 Facial clefting, oblique, 1 (OBLFC1) [MIM:600251] p.Gln415Pro

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)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

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

Disorders for SPECC1L Gene

MalaCards: The human disease database

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

Disorder Aliases PubMed IDs
facial clefting, oblique, 1
  • oblfc1
opitz gbbb syndrome, type ii
  • gbbb2
opitz-gbbb syndrome
  • hypertelorism with esophageal abnormality and hypospadias
oculomaxillofacial dysostosis
  • oculomaxillofacial dysplasia with oblique facial clefts
hypertelorism, teebi type
  • brachycephalofrontonasal dysplasia
- elite association - COSMIC cancer census association via MalaCards


  • 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.

Additional Disease Information for SPECC1L

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 58
  2. 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 58
  3. 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 58
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  5. Antigens recognized by autologous antibody in patients with renal-cell carcinoma. (PMID: 10508479) Scanlan MJ … Old LJ (International journal of cancer 1999) 3 4 58

Products for SPECC1L Gene

Sources for SPECC1L Gene

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