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    SYCP1 synaptonemal complex protein 1 [ Homo sapiens (human) ]

    Gene ID: 6847, updated on 3-Apr-2024

    Summary

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    Official Symbol
    SYCP1provided by HGNC
    Official Full Name
    synaptonemal complex protein 1provided by HGNC
    Primary source
    HGNC:HGNC:11487
    See related
    Ensembl:ENSG00000198765 MIM:602162; AllianceGenome:HGNC:11487
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CT8; SCP1; SCP-1; HOM-TES-14
    Summary
    Enables double-stranded DNA binding activity. Involved in protein homotetramerization. Predicted to be located in synaptonemal complex. Predicted to be active in central element; male germ cell nucleus; and transverse filament. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Restricted expression toward testis (RPKM 18.8) See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    1p13.2
    Exon count:
    38
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (114854088..114995370)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (114865527..115006795)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (115397484..115537991)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:115322492-115323058 Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:115323059-115323624 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:115332573-115333482 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:115333483-115334390 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:115337845-115338062 Neighboring gene suppressor of IKBKE 1 Neighboring gene MPRA-validated peak384 silencer Neighboring gene nuclear receptor subfamily 1 group H member 5, pseudogene Neighboring gene uncharacterized LOC105378915 Neighboring gene Sharpr-MPRA regulatory region 5363 Neighboring gene NANOG hESC enhancer GRCh37_chr1:115589292-115589828 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:115604953-115605476 Neighboring gene thyroid stimulating hormone subunit beta Neighboring gene uncharacterized LOC124904359 Neighboring gene tetraspanin 2

    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. A rare frameshift mutation in SYCP1 is associated with human male infertility. Nabi S, et al. Mol Hum Reprod, 2022 Apr 1. PMID 35377450
    2. Crystal Structure of C-Terminal Coiled-Coil Domain of SYCP1 Reveals Non-Canonical Anti-Parallel Dimeric Structure of Transverse Filament at the Synaptonemal Complex. Seo EK, et al. PLoS One, 2016. PMID 27548613, Free PMC Article
    3. X-ray crystallographic studies of the middle part of the human synaptonemal complex protein 1 coiled-coil domain. Park HH. Acta Crystallogr F Struct Biol Commun, 2015 Sep. PMID 26323297, Free PMC Article
    4. [Expression of cancer-testis antigen SCP-1 mRNA in human nasopharyngeal carcinoma]. Yi M, et al. Lin Chuang Er Bi Yan Hou Tou Jing Wai Ke Za Zhi, 2007 Apr. PMID 17608150
    5. Identification of an epitope derived from the cancer testis antigen HOM-TES-14/SCP1 and presented by dendritic cells to circulating CD4+ T cells. Neumann F, et al. Blood, 2005 Nov 1. PMID 16030183

    See all (27) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. A rare frameshift mutation in SYCP1 is associated with human male infertility.
      Title: A rare frameshift mutation in SYCP1 is associated with human male infertility.
    2. SYCP1 has an obligate tetrameric structure in which an N-terminal four-helical bundle bifurcates into two elongated C-terminal dimeric coiled-coils. This building block assembles into a zipper-like lattice through two self-assembly sites. N-terminal sites undergo cooperative head-to-head assembly in the midline, while C-terminal sites interact back to back on the chromosome axis.
      Title: Structural basis of meiotic chromosome synapsis through SYCP1 self-assembly.
    3. Crystal structure of C-terminal coiled-coil domain of SYCP1 reveals non-canonical anti-parallel dimeric structure of transverse filament at the synaptonemal complex.
      Title: Crystal Structure of C-Terminal Coiled-Coil Domain of SYCP1 Reveals Non-Canonical Anti-Parallel Dimeric Structure of Transverse Filament at the Synaptonemal Complex.
    4. crystal structure of the middle part of the human synaptonemal complex protein 1 coiled-coil domain
      Title: X-ray crystallographic studies of the middle part of the human synaptonemal complex protein 1 coiled-coil domain.
    5. SYCP1, cTAGE1, and GTSF1 are expressed in cutaneous T-cell lymphoma, but not in normal skin or benign inflammatory dermatoses.
      Title: Ectopic expression of cancer-testis antigens in cutaneous T-cell lymphoma patients.
    6. Cancer-Testis Antigen SCP-1 mRNA is expressed in some nasopharyngeal carcinoma.
      Title: [Expression of cancer-testis antigen SCP-1 mRNA in human nasopharyngeal carcinoma].
    7. Observational study of gene-disease association. (HuGE Navigator)
      Title: Investigation of genetic susceptibility factors for human longevity - a targeted nonsynonymous SNP study.
    8. an epitope derived from the cancer testis antigen HOM-TES-14/SCP1 and presented by dendritic cells to circulating CD4+ T cells
      Title: Identification of an epitope derived from the cancer testis antigen HOM-TES-14/SCP1 and presented by dendritic cells to circulating CD4+ T cells.
    Submit: New GeneRIF Correction

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC104417

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables double-stranded DNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables double-stranded DNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in cell division IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in chiasma assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in homologous chromosome pairing at meiosis ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in lateral element assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in meiotic DNA repair synthesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in protein homotetramerization IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in reciprocal meiotic recombination ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of protein localization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in sperm DNA condensation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in spermatogenesis TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in synaptonemal complex assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in autosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in central element IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in chromosome ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in chromosome, centromeric region IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in male germ cell nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in synaptonemal complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in transverse filament IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    synaptonemal complex protein 1
    Names
    cancer/testis antigen 8
    testicular tissue protein Li 191

    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.

    mRNA and Protein(s)

    1. NM_001282541.2 → NP_001269470.1  synaptonemal complex protein 1 isoform 1

      See identical proteins and their annotated locations for NP_001269470.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR. Both variants 1 and 2 encode the same isoform (1).
      Source sequence(s)
      AA868393, BC026162, BC144019, BI561137
      Consensus CDS
      CCDS879.1
      UniProtKB/Swiss-Prot
      O14963, Q15431, Q5VXJ6
      UniProtKB/TrEMBL
      A0A024R0I2, A0A140VJW4, B7ZLS9
      Related
      ENSP00000480997.1, ENST00000618516.4
      Conserved Domains (1) summary
      pfam05483
      Location:28 → 792
      SCP-1; Synaptonemal complex protein 1 (SCP-1)

    2. NM_001282542.2 → NP_001269471.1  synaptonemal complex protein 1 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and lacks an in-frame exon in the 3' coding region, compared to variant 1. The encoded isoform (2) is shorter, compared to isoform 1.
      Source sequence(s)
      AA868393, AK315268
      Consensus CDS
      CCDS72840.1
      UniProtKB/TrEMBL
      A0A087WZC3, B7ZLS9
      Related
      ENSP00000482532.1, ENST00000613524.4
      Conserved Domains (2) summary
      pfam05483
      Location:28 → 767
      SCP-1; Synaptonemal complex protein 1 (SCP-1)
      pfam07851
      Location:237 → 331
      TMPIT; TMPIT-like protein

    3. NM_003176.4 → NP_003167.2  synaptonemal complex protein 1 isoform 1

      See identical proteins and their annotated locations for NP_003167.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1). Both variants 1 and 2 encode the same isoform.
      Source sequence(s)
      AA868393, BC126266, BI561137
      Consensus CDS
      CCDS879.1
      UniProtKB/Swiss-Prot
      O14963, Q15431, Q5VXJ6
      UniProtKB/TrEMBL
      A0A024R0I2, A0A140VJW4, B7ZLS9
      Related
      ENSP00000358535.3, ENST00000369522.8
      Conserved Domains (1) summary
      pfam05483
      Location:28 → 792
      SCP-1; Synaptonemal complex protein 1 (SCP-1)

    RNA

    1. NR_104211.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) contains an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AA868393, BC026162, BC144020

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      114854088..114995370
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017002184.2 → XP_016857673.1  synaptonemal complex protein 1 isoform X1

      UniProtKB/Swiss-Prot
      O14963, Q15431, Q5VXJ6
      UniProtKB/TrEMBL
      A0A024R0I2, A0A140VJW4, B7ZLS9
      Conserved Domains (1) summary
      pfam05483
      Location:28 → 792
      SCP-1; Synaptonemal complex protein 1 (SCP-1)

    2. XM_005271156.2 → XP_005271213.1  synaptonemal complex protein 1 isoform X3

      UniProtKB/TrEMBL
      B7ZLS9
      Conserved Domains (2) summary
      pfam05483
      Location:28 → 737
      SCP-1; Synaptonemal complex protein 1 (SCP-1)
      pfam07851
      Location:182 → 276
      TMPIT; TMPIT-like protein

    3. XM_005271155.5 → XP_005271212.1  synaptonemal complex protein 1 isoform X2

      UniProtKB/TrEMBL
      B7ZLS9
      Conserved Domains (2) summary
      pfam05483
      Location:28 → 774
      SCP-1; Synaptonemal complex protein 1 (SCP-1)
      pfam07851
      Location:219 → 313
      TMPIT; TMPIT-like protein

    4. XM_011542037.3 → XP_011540339.1  synaptonemal complex protein 1 isoform X5

      UniProtKB/TrEMBL
      Q5VXJ5
      Related
      ENSP00000410011.1, ENST00000455987.5
      Conserved Domains (2) summary
      pfam05483
      Location:28 → 774
      SCP-1; Synaptonemal complex protein 1 (SCP-1)
      pfam07851
      Location:237 → 331
      TMPIT; TMPIT-like protein

    5. XM_011542039.2 → XP_011540341.1  synaptonemal complex protein 1 isoform X7

      Conserved Domains (2) summary
      pfam05483
      Location:28 → 549
      SCP-1; Synaptonemal complex protein 1 (SCP-1)
      pfam07851
      Location:237 → 331
      TMPIT; TMPIT-like protein

    6. XM_006710859.2 → XP_006710922.1  synaptonemal complex protein 1 isoform X1

      See identical proteins and their annotated locations for XP_006710922.1

      UniProtKB/Swiss-Prot
      O14963, Q15431, Q5VXJ6
      UniProtKB/TrEMBL
      A0A024R0I2, A0A140VJW4, B7ZLS9
      Related
      ENSP00000358531.1, ENST00000369518.1
      Conserved Domains (1) summary
      pfam05483
      Location:28 → 792
      SCP-1; Synaptonemal complex protein 1 (SCP-1)

    7. XM_011542038.2 → XP_011540340.1  synaptonemal complex protein 1 isoform X6

      Conserved Domains (2) summary
      pfam05483
      Location:1 → 581
      SCP-1; Synaptonemal complex protein 1 (SCP-1)
      pfam07851
      Location:26 → 120
      TMPIT; TMPIT-like protein

    8. XM_017002185.1 → XP_016857674.1  synaptonemal complex protein 1 isoform X4

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      114865527..115006795
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054338486.1 → XP_054194461.1  synaptonemal complex protein 1 isoform X1

    2. XM_054338488.1 → XP_054194463.1  synaptonemal complex protein 1 isoform X3

    3. XM_054338487.1 → XP_054194462.1  synaptonemal complex protein 1 isoform X2

    4. XM_054338490.1 → XP_054194465.1  synaptonemal complex protein 1 isoform X5

    5. XM_054338492.1 → XP_054194467.1  synaptonemal complex protein 1 isoform X7

    6. XM_054338485.1 → XP_054194460.1  synaptonemal complex protein 1 isoform X1

    7. XM_054338491.1 → XP_054194466.1  synaptonemal complex protein 1 isoform X6

    8. XM_054338489.1 → XP_054194464.1  synaptonemal complex protein 1 isoform X4

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q15431.2 GenPept UniProtKB/Swiss-Prot:Q15431

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