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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
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Genomic context

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See SYCP1 in Genome Data Viewer
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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