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LRRC20 leucine rich repeat containing 20 [ Homo sapiens (human) ]

Gene ID: 55222, updated on 3-Apr-2024

Summary

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Official Symbol
LRRC20provided by HGNC
Official Full Name
leucine rich repeat containing 20provided by HGNC
Primary source
HGNC:HGNC:23421
See related
Ensembl:ENSG00000172731 AllianceGenome:HGNC:23421
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
Broad expression in heart (RPKM 6.7), esophagus (RPKM 4.5) and 24 other tissues See more
Orthologs
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Genomic context

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Location:
10q22.1
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (70298975..70382625, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (71167949..71251681, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (72058731..72142381, complement)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:71981496-71981996 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:71981997-71982497 Neighboring gene inorganic pyrophosphatase 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2443 Neighboring gene H3K27me3-DHS negatively-acting regulatory element H2 Neighboring gene Sharpr-MPRA regulatory region 3619 Neighboring gene neuropeptide FF receptor 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3499 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72042967-72043468 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:72051346-72051556 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3500 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2444 Neighboring gene Sharpr-MPRA regulatory region 4423 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:72094756-72095256 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3501 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3502 Neighboring gene NANOG hESC enhancer GRCh37_chr10:72128656-72129157 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:72141592-72142211 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2445 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3504 Neighboring gene centrosomal protein 57 like 1 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2446 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2447 Neighboring gene eukaryotic translation initiation factor 4E binding protein 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. Genome-wide scan of healthy human connectome discovers SPON1 gene variant influencing dementia severity. Jahanshad N, et al. Proc Natl Acad Sci U S A, 2013 Mar 19. PMID 23471985, Free PMC Article
  2. Trait-stratified genome-wide association study identifies novel and diverse genetic associations with serologic and cytokine phenotypes in systemic lupus erythematosus. Kariuki SN, et al. Arthritis Res Ther, 2010. PMID 20659327, Free PMC Article
  3. The DNA sequence and comparative analysis of human chromosome 10. Deloukas P, et al. Nature, 2004 May 27. PMID 15164054
  4. A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease. Grupe A, et al. Am J Hum Genet, 2006 Jan. PMID 16385451, Free PMC Article
  5. Gsk3β and Tomm20 are substrates of the SCFFbxo7/PARK15 ubiquitin ligase associated with Parkinson's disease. Teixeira FR, et al. Biochem J, 2016 Oct 15. PMID 27503909, Free PMC Article

See all (20) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Observational study and genome-wide association study of gene-disease association. (HuGE Navigator)
    Title: Trait-stratified genome-wide association study identifies novel and diverse genetic associations with serologic and cytokine phenotypes in systemic lupus erythematosus.
  2. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
    Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
  3. Observational study of gene-disease association. (HuGE Navigator)
    Title: A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease.
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 scan of healthy human connectome discovers SPON1 gene variant influencing dementia severity.
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

Clone Names

  • FLJ10751, FLJ10844

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 

General protein information

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Preferred Names
leucine-rich repeat-containing protein 20

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_001278211.2 → NP_001265140.1  leucine-rich repeat-containing protein 20 isoform 1

    See identical proteins and their annotated locations for NP_001265140.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 1. Variants 1, 4, and 5 all encode the same isoform (1).
    Source sequence(s)
    AC022532, AL355138
    Consensus CDS
    CCDS7302.1
    UniProtKB/Swiss-Prot
    Q5T6D4, Q5T6D6, Q8TCA0, Q9NVA6, Q9NVG3
    UniProtKB/TrEMBL
    X6RK58
    Related
    ENSP00000362321.1, ENST00000373224.5
    Conserved Domains (4) summary
    PRK15370
    Location:7 → 184
    PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
    sd00031
    Location:76 → 98
    LRR_1; leucine-rich repeat [structural motif]
    sd00033
    Location:26 → 47
    LRR_RI; leucine-rich repeat [structural motif]
    cd21340
    Location:74 → 161
    PPP1R42; protein phosphatase 1 regulatory subunit 42

  2. NM_001278212.2 → NP_001265141.1  leucine-rich repeat-containing protein 20 isoform 1

    See identical proteins and their annotated locations for NP_001265141.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR compared to variant 1. Variants 1, 4, and 5 all encode the same isoform (1).
    Source sequence(s)
    AC022532, AL355138
    Consensus CDS
    CCDS7302.1
    UniProtKB/Swiss-Prot
    Q5T6D4, Q5T6D6, Q8TCA0, Q9NVA6, Q9NVG3
    UniProtKB/TrEMBL
    X6RK58
    Related
    ENSP00000413745.2, ENST00000446961.4
    Conserved Domains (4) summary
    PRK15370
    Location:7 → 184
    PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
    sd00031
    Location:76 → 98
    LRR_1; leucine-rich repeat [structural motif]
    sd00033
    Location:26 → 47
    LRR_RI; leucine-rich repeat [structural motif]
    cd21340
    Location:74 → 161
    PPP1R42; protein phosphatase 1 regulatory subunit 42

  3. NM_001278213.2 → NP_001265142.1  leucine-rich repeat-containing protein 20 isoform 2

    See identical proteins and their annotated locations for NP_001265142.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR and lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1. Variants 2 and 6 both encode the same isoform (2).
    Source sequence(s)
    AC022532, AL355138
    Consensus CDS
    CCDS7301.1
    Related
    ENSP00000378458.1, ENST00000395011.5
    Conserved Domains (2) summary
    sd00031
    Location:28 → 48
    LRR_1; leucine-rich repeat [structural motif]
    pfam13855
    Location:48 → 106
    LRR_8; Leucine rich repeat

  4. NM_001278214.2 → NP_001265143.1  leucine-rich repeat-containing protein 20 isoform 4

    See identical proteins and their annotated locations for NP_001265143.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (7) differs in the 5' UTR and lacks the exon containing the translation start codon compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (4) with a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AC022532, AL355138
    Consensus CDS
    CCDS73145.1
    UniProtKB/TrEMBL
    A0A0A0MS58
    Related
    ENSP00000378457.2, ENST00000395010.5
    Conserved Domains (2) summary
    sd00031
    Location:7 → 29
    LRR_1; leucine-rich repeat [structural motif]
    cd21340
    Location:5 → 92
    PPP1R42; protein phosphatase 1 regulatory subunit 42

  5. NM_018205.4 → NP_060675.1  leucine-rich repeat-containing protein 20 isoform 3

    See identical proteins and their annotated locations for NP_060675.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and lacks an alternate in-frame exon compared to variant 1. The resulting isoform (3) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AC022532, AL355138
    Consensus CDS
    CCDS7300.1
    Related
    ENSP00000350255.2, ENST00000357631.6

  6. NM_018239.4 → NP_060709.2  leucine-rich repeat-containing protein 20 isoform 2

    See identical proteins and their annotated locations for NP_060709.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR and lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1. Variants 2 and 6 both encode the same isoform (2).
    Source sequence(s)
    AC022532, AL355138
    Consensus CDS
    CCDS7301.1
    Related
    ENSP00000350860.2, ENST00000358141.6
    Conserved Domains (2) summary
    sd00031
    Location:28 → 48
    LRR_1; leucine-rich repeat [structural motif]
    pfam13855
    Location:48 → 106
    LRR_8; Leucine rich repeat

  7. NM_207119.3 → NP_997002.1  leucine-rich repeat-containing protein 20 isoform 1

    See identical proteins and their annotated locations for NP_997002.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1). Variants 1, 4, and 5 all encode the same isoform (1).
    Source sequence(s)
    AC022532, AL355138
    Consensus CDS
    CCDS7302.1
    UniProtKB/Swiss-Prot
    Q5T6D4, Q5T6D6, Q8TCA0, Q9NVA6, Q9NVG3
    UniProtKB/TrEMBL
    X6RK58
    Related
    ENSP00000348043.4, ENST00000355790.8
    Conserved Domains (4) summary
    PRK15370
    Location:7 → 184
    PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
    sd00031
    Location:76 → 98
    LRR_1; leucine-rich repeat [structural motif]
    sd00033
    Location:26 → 47
    LRR_RI; leucine-rich repeat [structural motif]
    cd21340
    Location:74 → 161
    PPP1R42; protein phosphatase 1 regulatory subunit 42

RNA

  1. NR_103467.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (8) differs in the 5' UTR, lacks the exon containing the translation start codon, and lacks an alternate in-frame exon compared to variant 1. This variant is represented as non-coding because it lacks a large portion of the coding region, including the translational start codon, found in variant 1.
    Source sequence(s)
    AC022532, AL355138

  2. NR_103468.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (9) differs in the 5' UTR, lacks the exon containing the translation start codon, and lacks an alternate in-frame exon compared to variant 1. This variant is represented as non-coding because it lacks a large portion of the coding region, including the translational start codon, found in variant 1.
    Source sequence(s)
    AC022532, AL355138

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_000010.11 Reference GRCh38.p14 Primary Assembly

    Range
    70298975..70382625 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047425418.1 → XP_047281374.1  leucine-rich repeat-containing protein 20 isoform X2

  2. XM_047425421.1 → XP_047281377.1  leucine-rich repeat-containing protein 20 isoform X3

  3. XM_047425417.1 → XP_047281373.1  leucine-rich repeat-containing protein 20 isoform X2

  4. XM_047425419.1 → XP_047281375.1  leucine-rich repeat-containing protein 20 isoform X3

  5. XM_017016375.2 → XP_016871864.1  leucine-rich repeat-containing protein 20 isoform X1

    UniProtKB/Swiss-Prot
    Q5T6D4, Q5T6D6, Q8TCA0, Q9NVA6, Q9NVG3
    UniProtKB/TrEMBL
    X6RK58
    Conserved Domains (4) summary
    PRK15370
    Location:7 → 184
    PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
    sd00031
    Location:76 → 98
    LRR_1; leucine-rich repeat [structural motif]
    sd00033
    Location:26 → 47
    LRR_RI; leucine-rich repeat [structural motif]
    cd21340
    Location:74 → 161
    PPP1R42; protein phosphatase 1 regulatory subunit 42

  6. XM_047425420.1 → XP_047281376.1  leucine-rich repeat-containing protein 20 isoform X3

  7. XM_017016374.2 → XP_016871863.1  leucine-rich repeat-containing protein 20 isoform X1

    UniProtKB/Swiss-Prot
    Q5T6D4, Q5T6D6, Q8TCA0, Q9NVA6, Q9NVG3
    UniProtKB/TrEMBL
    X6RK58
    Conserved Domains (4) summary
    PRK15370
    Location:7 → 184
    PRK15370; type III secretion system effector E3 ubiquitin transferase SlrP
    sd00031
    Location:76 → 98
    LRR_1; leucine-rich repeat [structural motif]
    sd00033
    Location:26 → 47
    LRR_RI; leucine-rich repeat [structural motif]
    cd21340
    Location:74 → 161
    PPP1R42; protein phosphatase 1 regulatory subunit 42

  8. XM_047425422.1 → XP_047281378.1  leucine-rich repeat-containing protein 20 isoform X4

    UniProtKB/TrEMBL
    A0A0A0MS58

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060934.1 Alternate T2T-CHM13v2.0

    Range
    71167949..71251681 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054366201.1 → XP_054222176.1  leucine-rich repeat-containing protein 20 isoform X2

  2. XM_054366204.1 → XP_054222179.1  leucine-rich repeat-containing protein 20 isoform X3

  3. XM_054366199.1 → XP_054222174.1  leucine-rich repeat-containing protein 20 isoform X1

    UniProtKB/Swiss-Prot
    Q5T6D4, Q5T6D6, Q8TCA0, Q9NVA6, Q9NVG3

  4. XM_054366200.1 → XP_054222175.1  leucine-rich repeat-containing protein 20 isoform X2

  5. XM_054366202.1 → XP_054222177.1  leucine-rich repeat-containing protein 20 isoform X3

  6. XM_054366203.1 → XP_054222178.1  leucine-rich repeat-containing protein 20 isoform X3

  7. XM_054366198.1 → XP_054222173.1  leucine-rich repeat-containing protein 20 isoform X1

    UniProtKB/Swiss-Prot
    Q5T6D4, Q5T6D6, Q8TCA0, Q9NVA6, Q9NVG3

  8. XM_054366205.1 → XP_054222180.1  leucine-rich repeat-containing protein 20 isoform X4

    UniProtKB/TrEMBL
    A0A0A0MS58
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8TCA0.1 GenPept UniProtKB/Swiss-Prot:Q8TCA0

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