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SPECC1L sperm antigen with calponin homology and coiled-coil domains 1 like [ Homo sapiens (human) ]

Gene ID: 23384, updated on 27-Nov-2024

Summary

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Official Symbol
SPECC1Lprovided by HGNC
Official Full Name
sperm antigen with calponin homology and coiled-coil domains 1 likeprovided by HGNC
Primary source
HGNC:HGNC:29022
See related
Ensembl:ENSG00000100014 MIM:614140; AllianceGenome:HGNC:29022
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
TBHS; CYTSA; GBBB2; TBHS1; OBLFC1
Summary
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]
Expression
Ubiquitous expression in testis (RPKM 21.3), thyroid (RPKM 13.1) and 25 other tissues See more
Orthologs
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Genomic context

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See SPECC1L in Genome Data Viewer
Location:
22q11.23
Exon count:
19
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 22 NC_000022.11 (24270831..24417738)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 22 NC_060946.1 (24732441..24879351)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 22 NC_000022.10 (24666799..24813706)

Chromosome 22 - NC_000022.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:24655631-24656248 Neighboring gene SPECC1L-ADORA2A readthrough (NMD candidate) Neighboring gene POM121 transmembrane nucleoporin like 9, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:24660235-24660965 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13547 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18767 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18768 Neighboring gene BCR pseudogene 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr22:24680125-24680630 Neighboring gene ribosomal protein S10 pseudogene 29 Neighboring gene Sharpr-MPRA regulatory region 3008 Neighboring gene Sharpr-MPRA regulatory region 3699 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr22:24712259-24712996 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:24734941-24735636 Neighboring gene uncharacterized LOC105372960 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18769 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:24804357-24804858 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:24804859-24805358 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:24813636-24813812 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:24814323-24814932 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:24816151-24816760 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:24817371-24817980 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13549 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13548 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:24820284-24820935 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr22:24820936-24821586 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13550 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18770 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:24825428-24826389 Neighboring gene ADORA2A antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:24829365-24829914 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18771 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:24831043-24831543 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13551 Neighboring gene adenosine A2a receptor Neighboring gene ReSE screen-validated silencer GRCh37_chr22:24840685-24840876 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13552 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18772 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18773 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:24875502-24875689 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18774 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:24901494-24902032 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr22:24902033-24902569 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18775 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18776 Neighboring gene ReSE screen-validated silencer GRCh37_chr22:24905414-24905687 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18777 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13553 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18778 Neighboring gene beta-ureidopropionase 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: 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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Related articles in PubMed

  1. Translocation (1;22) in a child with bilateral oblique facial clefts. Dasouki M, et al. J Med Genet, 1988 Jun. PMID 3398011, Free PMC Article
  2. Expanding the SPECC1L mutation phenotypic spectrum to include Teebi hypertelorism syndrome. Bhoj EJ, et al. Am J Med Genet A, 2015 Nov. PMID 26111080
  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. Kruszka P, et al. J Med Genet, 2015 Feb. PMID 25412741, Free PMC Article
  4. Congenital diaphragmatic hernia as a prominent feature of a SPECC1L-related syndrome. Wild KT, et al. Am J Med Genet A, 2020 Dec. PMID 32954677, Free PMC Article
  5. SPECC1L Mutations Are Not Common in Sporadic Cases of Opitz G/BBB Syndrome. Migliore C, et al. Genes (Basel), 2022 Jan 28. PMID 35205294, Free PMC Article

See all (94) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Changes in expression of VGF, SPECC1L, HLA-DRA and RANBP3L act with APOE E4 to alter risk for late onset Alzheimer's disease.
    Title: Changes in expression of VGF, SPECC1L, HLA-DRA and RANBP3L act with APOE E4 to alter risk for late onset Alzheimer's disease.
  2. SPECC1L: a cytoskeletal protein that regulates embryonic tissue dynamics.
    Title: SPECC1L: a cytoskeletal protein that regulates embryonic tissue dynamics.
  3. SPECC1L binds the myosin phosphatase complex MYPT1/PP1beta and can regulate its distribution between microtubules and filamentous actin.
    Title: SPECC1L binds the myosin phosphatase complex MYPT1/PP1β and can regulate its distribution between microtubules and filamentous actin.
  4. BCL6-SPECC1L: A Novel Fusion Gene in Nasopharyngeal Carcinoma.
    Title: BCL6-SPECC1L: A Novel Fusion Gene in Nasopharyngeal Carcinoma.
  5. SPECC1L Mutations Are Not Common in Sporadic Cases of Opitz G/BBB Syndrome.
    Title: SPECC1L Mutations Are Not Common in Sporadic Cases of Opitz G/BBB Syndrome.
  6. Recurrent SPECC1L-NTRK fusions in pediatric sarcoma and brain tumors.
    Title: Recurrent SPECC1L-NTRK fusions in pediatric sarcoma and brain tumors.
  7. SPECC1L regulates palate development downstream of IRF6.
    Title: SPECC1L regulates palate development downstream of IRF6.
  8. Congenital diaphragmatic hernia as a prominent feature of a SPECC1L-related syndrome.
    Title: Congenital diaphragmatic hernia as a prominent feature of a SPECC1L-related syndrome.
  9. SPECC1L as a novel modulator of PI3K-AKT signaling and AJ biology, required for neural tube closure and CNCC delamination.
    Title: SPECC1L deficiency results in increased adherens junction stability and reduced cranial neural crest cell delamination.
  10. two unrelated families with a Teebi hypertelorism-like syndrome and Teebi hypertelorism phenotype who have missense mutations in Sperm Antigen With Calponin Homology And Coiled-Coil Domains (SPECC1L), are reported.
    Title: Expanding the SPECC1L mutation phenotypic spectrum to include Teebi hypertelorism syndrome.
Submit: New GeneRIF Correction See all GeneRIFs (14)

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
Oculomaxillofacial dysostosis
MedGen: C1838348 OMIM: 600251 GeneReviews: Not available
Compare labs
Teebi hypertelorism syndrome 1
MedGen: CN306405 OMIM: 145420 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

Description
Genome-wide association study identifies three novel susceptibility loci for severe Acne vulgaris.
EBI GWAS Catalog

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

Readthrough SPECC1L-ADORA2A

Readthrough gene: SPECC1L-ADORA2A, Included gene: ADORA2A

Homology

Clone Names

  • KIAA0376

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in actin cytoskeleton organization IBA
Inferred from Biological aspect of Ancestor
more info
  
acts_upstream_of_or_within cell adhesion IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in cell division IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in actin cytoskeleton IDA
Inferred from Direct Assay
more info
  
located_in cytoplasm IEA
Inferred from Electronic Annotation
more info
  
part_of filamentous actin IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in gap junction IEA
Inferred from Electronic Annotation
more info
  
is_active_in microtubule organizing center IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in spindle IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
cytospin-A
Names
SPECC1-like protein
cytokinesis and spindle organization A
renal carcinoma antigen NY-REN-22

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

  1. NG_031915.3 RefSeqGene

    Range
    5002..151909
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001145468.4 → NP_001138940.4  cytospin-A isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an exon in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same isoform (1).
    Source sequence(s)
    AP000354, AP000355, KC877946
    Consensus CDS
    CCDS33619.1
    UniProtKB/Swiss-Prot
    B7Z758, F5H1H6, O15081, Q69YQ0
    UniProtKB/TrEMBL
    B2RMV2
    Related
    ENSP00000393363.1, ENST00000437398.5
    Conserved Domains (4) summary
    PHA03247
    Location:827 → 992
    PHA03247; large tegument protein UL36; Provisional
    COG1196
    Location:500 → 801
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
    cd21199
    Location:1005 → 1116
    CH_CYTS; calponin homology (CH) domain found in the cytospin family
    pfam15921
    Location:172 → 802
    CCDC158; Coiled-coil domain-containing protein 158

  2. NM_001254732.3 → NP_001241661.3  cytospin-A isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and lacks an exon in the 3' coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AP000354, AP000355, KC877946
    Consensus CDS
    CCDS58797.1
    UniProtKB/TrEMBL
    B2RMV2
    Related
    ENSP00000439633.1, ENST00000541492.1
    Conserved Domains (4) summary
    PHA03247
    Location:827 → 992
    PHA03247; large tegument protein UL36; Provisional
    COG1196
    Location:500 → 801
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
    pfam12128
    Location:176 → 803
    DUF3584; Protein of unknown function (DUF3584)
    cl00030
    Location:999 → 1078
    CH_SF; calponin homology (CH) domain superfamily

  3. NM_001254733.2 → NP_001241662.2  cytospin-A isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream, in-frame start codon, compared to variant 1. The encoded isoform (3) has a shorter N-terminus, compared to isoform 1.
    Source sequence(s)
    AP000354, AP000355
    Conserved Domains (1) summary
    cd21199
    Location:71 → 182
    CH_CYTS; calponin homology (CH) domain found in the cytospin family

  4. NM_015330.6 → NP_056145.5  cytospin-A isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript. Variants 1 and 2 encode the same isoform (1).
    Source sequence(s)
    AL832425, AP000354, BC013085, BC021132, BM126792, HY105216
    Consensus CDS
    CCDS33619.1
    UniProtKB/Swiss-Prot
    B7Z758, F5H1H6, O15081, Q69YQ0
    UniProtKB/TrEMBL
    B2RMV2
    Related
    ENSP00000325785.8, ENST00000314328.14
    Conserved Domains (4) summary
    PHA03247
    Location:827 → 992
    PHA03247; large tegument protein UL36; Provisional
    COG1196
    Location:500 → 801
    Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
    cd21199
    Location:1005 → 1116
    CH_CYTS; calponin homology (CH) domain found in the cytospin family
    pfam15921
    Location:172 → 802
    CCDC158; Coiled-coil domain-containing protein 158

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

  1. NC_000022.11 Reference GRCh38.p14 Primary Assembly

    Range
    24270831..24417738
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060946.1 Alternate T2T-CHM13v2.0

    Range
    24732441..24879351
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q69YQ0.3 GenPept UniProtKB/Swiss-Prot:Q69YQ0

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