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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
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Genomic context

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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.

Chemical Information
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