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LEKR1 leucine, glutamate and lysine rich 1 [ Homo sapiens (human) ]

Gene ID: 389170, updated on 27-Nov-2024

Summary

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Official Symbol
LEKR1provided by HGNC
Official Full Name
leucine, glutamate and lysine rich 1provided by HGNC
Primary source
HGNC:HGNC:33765
See related
Ensembl:ENSG00000197980 MIM:613536; AllianceGenome:HGNC:33765
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
Expression
Biased expression in testis (RPKM 1.9), thyroid (RPKM 0.4) and 7 other tissues See more
Orthologs
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Genomic context

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See LEKR1 in Genome Data Viewer
Location:
3q25.31
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (156826353..157046129)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (159601066..159820688)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (156544142..156763918)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene methyltransferase like 15 pseudogene 1 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:156468641-156469394 Neighboring gene long intergenic non-protein coding RNA 886 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20732 Neighboring gene Sharpr-MPRA regulatory region 2365 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14839 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr3:156534749-156535948 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14841 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20733 Neighboring gene Sharpr-MPRA regulatory region 161 Neighboring gene proliferation-associated 2G4 pseudogene 4 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:156684212-156684369 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20734 Neighboring gene KLF3 pseudogene 2 Neighboring gene CRADD pseudogene 1 Neighboring gene RN7SK pseudogene 177 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:156760074-156760241 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14842 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20735 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14843 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20736 Neighboring gene long intergenic non-protein coding RNA 880 Neighboring gene long intergenic non-protein coding RNA 2029 Neighboring gene long intergenic non-protein coding RNA 881

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. Genetic variants in LEKR1 and GALNT10 modulate sex-difference in carotid intima-media thickness: a genome-wide interaction study. Dong C, et al. Atherosclerosis, 2015 Jun. PMID 25898001, Free PMC Article
  2. The chromosome 3q25 genomic region is associated with measures of adiposity in newborns in a multi-ethnic genome-wide association study. Urbanek M, et al. Hum Mol Genet, 2013 Sep 1. PMID 23575227, Free PMC Article
  3. The birth weight lowering C-allele of rs900400 near LEKR1 and CCNL1 associates with elevated insulin release following an oral glucose challenge. Andersson EA, et al. PLoS One, 2011. PMID 22073261, Free PMC Article
  4. Variants in ADCY5 and near CCNL1 are associated with fetal growth and birth weight. Freathy RM, et al. Nat Genet, 2010 May. PMID 20372150, Free PMC Article
  5. Association between LEKR1-CCNL1 and IGSF21-KLHDC7A gene polymorphisms and diabetic retinopathy of type 2 diabetes mellitus in the Chinese Han population. Lin X, et al. J Gene Med, 2016 Oct. PMID 27607899

See all (16) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Results suggest that LEKR1-CCNL1 and IGSF21-KLHDC7A gene polymorphisms influence the development of diabetic retinopathy (DR).
    Title: Association between LEKR1-CCNL1 and IGSF21-KLHDC7A gene polymorphisms and diabetic retinopathy of type 2 diabetes mellitus in the Chinese Han population.
  2. SNPs in LEKR1 and GALNT10 modulate sex-difference in carotid intima-media thickness.
    Title: Genetic variants in LEKR1 and GALNT10 modulate sex-difference in carotid intima-media thickness: a genome-wide interaction study.
  3. birth weight lowering effect of the C-allele of rs900400 located near LEKR1 and CCNL1 was replicated in the Danish population. Furthermore the C-allele was associated with increased insulin response following oral glucose stimulation
    Title: The birth weight lowering C-allele of rs900400 near LEKR1 and CCNL1 associates with elevated insulin release following an oral glucose challenge.
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
Genome-wide association analysis of eating disorder-related symptoms, behaviors, and personality traits.
EBI GWAS Catalog
Genome-wide association analysis of susceptibility and clinical phenotype in multiple sclerosis.
EBI GWAS Catalog
Genome-wide meta-analysis for severe diabetic retinopathy.
EBI GWAS Catalog
Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture.
EBI GWAS Catalog
Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.
EBI GWAS Catalog
The chromosome 3q25 genomic region is associated with measures of adiposity in newborns in a multi-ethnic genome-wide association study.
EBI GWAS Catalog
Variants in ADCY5 and near CCNL1 are associated with fetal growth and birth weight.
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

Homology

Clone Names

  • FLJ16641, FLJ37161

General protein information

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Preferred Names
protein LEKR1
Names
leucine-, glutamate- and lysine-rich protein 1

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_001004316.3 → NP_001004316.2  protein LEKR1 isoform 1

    See identical proteins and their annotated locations for NP_001004316.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1). It should be noted that this exon combination lacks full-length transcript support; it is predicted based on partial human and orthologous transcript alignments.
    Source sequence(s)
    AC092993, AC106708, AC117392
    UniProtKB/TrEMBL
    J3KP02
    Related
    ENSP00000348936.4, ENST00000356539.9
    Conserved Domains (1) summary
    cl23765
    Location:470 → 592
    iSH2_PI3K_IA_R; Inter-Src homology 2 (iSH2) helical domain of Class IA Phosphoinositide 3-kinase Regulatory subunits

  2. NM_001193283.2 → NP_001180212.1  protein LEKR1 isoform 2

    See identical proteins and their annotated locations for NP_001180212.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' and 3' UTRs, and lacks several exons in the 3' coding region but includes an alternate 3' exon, compared to variant 1. The resulting isoform (2) has a distinct and shorter C-terminus, compared to isoform 1.
    Source sequence(s)
    AC106708, BC041967, DA075031
    Consensus CDS
    CCDS54660.1
    UniProtKB/Swiss-Prot
    D3DNK8, Q6ZMV7, S4R3D4
    Related
    ENSP00000474182.1, ENST00000491763.1

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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    156826353..157046129
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    159601066..159820688
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6ZMV7.3 GenPept UniProtKB/Swiss-Prot:Q6ZMV7

Gene LinkOut

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

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