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    SYCP2L synaptonemal complex protein 2 like [ Homo sapiens (human) ]

    Gene ID: 221711, updated on 11-Apr-2024

    Summary

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    Official Symbol
    SYCP2Lprovided by HGNC
    Official Full Name
    synaptonemal complex protein 2 likeprovided by HGNC
    Primary source
    HGNC:HGNC:21537
    See related
    Ensembl:ENSG00000153157 MIM:616799; AllianceGenome:HGNC:21537
    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
    NO145; C6orf177; dJ62D2.1
    Summary
    Predicted to be involved in meiotic nuclear division. Predicted to act upstream of or within negative regulation of cell death. Located in condensed chromosome, centromeric region and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Broad expression in testis (RPKM 2.2), placenta (RPKM 0.6) and 16 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SYCP2L in Genome Data Viewer
    Location:
    6p24.2
    Exon count:
    30
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (10887052..10974309)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (10754685..10841961)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (10887285..10974542)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene male germ cell associated kinase Neighboring gene ReSE screen-validated silencer GRCh37_chr6:10814688-10814873 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16907 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23973 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23974 Neighboring gene Sharpr-MPRA regulatory region 8043 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:10886452-10887220 Neighboring gene glial cells missing transcription factor 2 Neighboring gene uncharacterized LOC101928191 Neighboring gene Sharpr-MPRA regulatory region 7443 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:10963174-10963734 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:10976416-10976916 Neighboring gene ELOVL fatty acid elongase 2 Neighboring gene siah E3 ubiquitin protein ligase family member 3 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16908 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:11045068-11045568 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:11045569-11046069 Neighboring gene ELOVL2 antisense RNA 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. Homozygous variants in SYCP2L cause premature ovarian insufficiency. He WB, et al. J Med Genet, 2021 Mar. PMID 32303603, Free PMC Article
    2. Accelerated reproductive aging in females lacking a novel centromere protein SYCP2L. Zhou J, et al. Hum Mol Genet, 2015 Nov 15. PMID 26362258, Free PMC Article
    3. Genome-wide association studies identify loci associated with age at menarche and age at natural menopause. He C, et al. Nat Genet, 2009 Jun. PMID 19448621, Free PMC Article
    4. Meta-analyses identify 13 loci associated with age at menopause and highlight DNA repair and immune pathways. Stolk L, et al. Nat Genet, 2012 Jan 22. PMID 22267201, Free PMC Article
    5. Integrated genome-wide association, coexpression network, and expression single nucleotide polymorphism analysis identifies novel pathway in allergic rhinitis. Bunyavanich S, et al. BMC Med Genomics, 2014 Aug 2. PMID 25085501, Free PMC Article

    See all (15) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Involvement of SYCP2L and TDRD3 gene variants on ovarian reserve and reproductive outcomes: a cross-sectional study.
      Title: Involvement of SYCP2L and TDRD3 gene variants on ovarian reserve and reproductive outcomes: a cross-sectional study.
    2. Homozygous variants in SYCP2L cause premature ovarian insufficiency.
      Title: Homozygous variants in SYCP2L cause premature ovarian insufficiency.
    3. We find that a human SYCP2L intronic single nucleotide polymorphism (SNP) rs2153157, which is associated with ANM, changes the splicing efficiency of U12-type minor introns
      Title: Accelerated reproductive aging in females lacking a novel centromere protein SYCP2L.
    4. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
      Title: Genome-wide association studies identify loci associated with age at menarche and age at natural menopause.
    Submit: New GeneRIF Correction

    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

    EBI GWAS Catalog

    Description
    Genetic loci associated with plasma phospholipid n-3 fatty acids: a meta-analysis of genome-wide association studies from the CHARGE Consortium.
    EBI GWAS Catalog
    Genome-wide association studies identify loci associated with age at menarche and age at natural menopause.
    EBI GWAS Catalog
    Genome-wide association study on dimethylarginines reveals novel AGXT2 variants associated with heart rate variability but not with overall mortality.
    EBI GWAS Catalog
    Integrated Genome-wide Association, Coexpression Network, and Expression Single Nucleotide Polymorphism Analysis Identifies Novel Pathway in Allergic Rhinitis.
    EBI GWAS Catalog
    Meta-analyses identify 13 loci associated with age at menopause and highlight DNA repair and immune pathways.
    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)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Process Evidence Code Pubs
    involved_in meiotic nuclear division IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in mitotic G1 phase IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of programmed cell death IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in condensed chromosome, centromeric region IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in condensed chromosome, centromeric region IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in female germ cell nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in lateral element IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    synaptonemal complex protein 2-like
    Names
    145 kDa nucleolar protein homolog
    SCP-2-like

    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_001040274.3 → NP_001035364.2  synaptonemal complex protein 2-like

      See identical proteins and their annotated locations for NP_001035364.2

      Status: VALIDATED

      Source sequence(s)
      AI027433, AK294018, AL357497, AM293674, DB077181
      Consensus CDS
      CCDS43423.1
      UniProtKB/Swiss-Prot
      A6NDS5, Q08GK5, Q5T4T6, Q6ZRM2, Q96EJ2
      Related
      ENSP00000283141.6, ENST00000283141.11

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      10887052..10974309
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      10754685..10841961
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_194299.1: Suppressed sequence

      Description
      NM_194299.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q5T4T6.2 GenPept UniProtKB/Swiss-Prot:Q5T4T6

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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