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    LRMDA leucine rich melanocyte differentiation associated [ Homo sapiens (human) ]

    Gene ID: 83938, updated on 5-Mar-2024

    Summary

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    Official Symbol
    LRMDAprovided by HGNC
    Official Full Name
    leucine rich melanocyte differentiation associatedprovided by HGNC
    Primary source
    HGNC:HGNC:23405
    See related
    Ensembl:ENSG00000148655 MIM:614537; AllianceGenome:HGNC:23405
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    CDA017; C10orf11
    Summary
    This gene encodes a leucine-rich repeat protein. The encoded protein is thought to play a role in melanocyte differentiation. Mutations in this gene have been associated with autosomal recessive oculocutaneous albinism 7 (OCA7). Alternatively spliced transcript variants have been identified. [provided by RefSeq, Mar 2015]
    Expression
    Ubiquitous expression in adrenal (RPKM 1.6), spleen (RPKM 0.7) and 24 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    10q22.2-q22.3
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (75431624..76560168)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (76305674..77428762)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (77191382..78319926)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101929234 Neighboring gene uncharacterized LOC107984293 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:77191691-77192191 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr10:77191190-77191690 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:77210325-77211210 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:77234571-77235319 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:77235320-77236067 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:77297811-77298425 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr10:77356902-77357728 Neighboring gene NANOG hESC enhancer GRCh37_chr10:77359991-77360570 Neighboring gene uncharacterized LOC105378367 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:77488076-77488220 Neighboring gene microRNA 606 Neighboring gene NANOG hESC enhancer GRCh37_chr10:77509344-77509845 Neighboring gene Sharpr-MPRA regulatory region 10683 Neighboring gene uncharacterized LOC124902463 Neighboring gene VISTA enhancer hs320 Neighboring gene VISTA enhancer hs1679 Neighboring gene NANOG hESC enhancer GRCh37_chr10:77810766-77811299 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:77841543-77842122 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:77842123-77842700 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:77843280-77843857 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr10:77862769-77863468 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:77872187-77872740 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:77909300-77910208 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:77990417-77991136 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr10:77991137-77991854 Neighboring gene Sharpr-MPRA regulatory region 15163 Neighboring gene uncharacterized LOC124902462 Neighboring gene Sharpr-MPRA regulatory region 11048 Neighboring gene uncharacterized LOC112268057 Neighboring gene RNA, 7SL, cytoplasmic 518, pseudogene Neighboring gene Sharpr-MPRA regulatory region 6857 Neighboring gene RNA, U6 small nuclear 673, pseudogene Neighboring gene VISTA enhancer hs1683 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:78192871-78193568 Neighboring gene VISTA enhancer hs1434 Neighboring gene Sharpr-MPRA regulatory region 3593 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr10:78383798-78384997 Neighboring gene VISTA enhancer hs748 Neighboring gene NANOG hESC enhancer GRCh37_chr10:78538831-78539723 Neighboring gene OCT4 hESC enhancer GRCh37_chr10:78568996-78569497 Neighboring gene NANOG hESC enhancer GRCh37_chr10:78582741-78583242 Neighboring gene ATP synthase membrane subunit c locus 1 pseudogene 8 Neighboring gene uncharacterized LOC124902466 Neighboring gene KCNMA1 antisense RNA 1 Neighboring gene potassium calcium-activated channel subfamily M alpha 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. A genome-wide association study identifies locus at 10q22 associated with clinical outcomes of adjuvant tamoxifen therapy for breast cancer patients in Japanese. Kiyotani K, et al. Hum Mol Genet, 2012 Apr 1. PMID 22180457
    2. Chromosome aberrations involving 10q22: report of three overlapping interstitial deletions and a balanced translocation disrupting C10orf11. Tzschach A, et al. Eur J Hum Genet, 2010 Mar. PMID 19844253, Free PMC Article
    3. Mutations in c10orf11, a melanocyte-differentiation gene, cause autosomal-recessive albinism. Grønskov K, et al. Am J Hum Genet, 2013 Mar 7. PMID 23395477, Free PMC Article
    4. Germline genetic variation in an organic anion transporter polypeptide associated with methotrexate pharmacokinetics and clinical effects. Treviño LR, et al. J Clin Oncol, 2009 Dec 10. PMID 19901119, Free PMC Article
    5. Oculocutaneous Albinism and Ocular Albinism Overview. Adam MP, et al. , 1993. PMID 37053367

    See all (17) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. 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.
    2. This finding suggests that haploinsufficiency of C10orf11 contributes to the cognitive defects in 10q22 deletion patients.
      Title: Chromosome aberrations involving 10q22: report of three overlapping interstitial deletions and a balanced translocation disrupting C10orf11.
    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
    A genome-wide association study identifies locus at 10q22 associated with clinical outcomes of adjuvant tamoxifen therapy for breast cancer patients in Japanese.
    EBI GWAS Catalog
    Genetic variants associated with disordered eating.
    EBI GWAS Catalog
    Genome-wide association and large-scale follow up identifies 16 new loci influencing lung function.
    EBI GWAS Catalog
    Genome-wide association study of lung function phenotypes in a founder population.
    EBI GWAS Catalog
    Genome-wide joint meta-analysis of SNP and SNP-by-smoking interaction identifies novel loci for pulmonary function.
    EBI GWAS Catalog
    Germline genetic variation in an organic anion transporter polypeptide associated with methotrexate pharmacokinetics and clinical effects.
    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 melanocyte differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in melanocyte differentiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    leucine-rich melanocyte differentiation-associated protein
    Names
    leucine-rich repeat-containing protein C10orf11

    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.

    Genomic

    1. NG_042180.2 RefSeqGene

      Range
      5002..1133546
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001305581.2 → NP_001292510.1  leucine-rich melanocyte differentiation-associated protein isoform 1

      See identical proteins and their annotated locations for NP_001292510.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AC010997, AC012047, AC024603, BM720401, BX105111, CR933639, HY006640
      Consensus CDS
      CCDS76319.1
      UniProtKB/TrEMBL
      A0A087WWI0
      Related
      ENSP00000480240.1, ENST00000611255.5
      Conserved Domains (4) summary
      cd00116
      Location:27 → 113
      LRR_RI; Leucine-rich repeats (LRRs), ribonuclease inhibitor (RI)-like subfamily. LRRs are 20-29 residue sequence motifs present in many proteins that participate in protein-protein interactions and have different functions and cellular locations. LRRs correspond ...
      sd00031
      Location:34 → 54
      LRR_1; leucine-rich repeat [structural motif]
      pfam12799
      Location:54 → 93
      LRR_4; Leucine Rich repeats (2 copies)
      pfam13855
      Location:53 → 112
      LRR_8; Leucine rich repeat

    2. NM_032024.5 → NP_114413.1  leucine-rich melanocyte differentiation-associated protein isoform 2

      See identical proteins and their annotated locations for NP_114413.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (2) has a distinct N-terminus and is shorter than isoform 1.
      Source sequence(s)
      AC024603, AF267860, CR933639
      Consensus CDS
      CCDS7351.1
      UniProtKB/Swiss-Prot
      B1AVW6, Q9H2I8
      Related
      ENSP00000361577.1, ENST00000372499.5
      Conserved Domains (4) summary
      sd00031
      Location:3 → 26
      LRR_1; leucine-rich repeat [structural motif]
      pfam12799
      Location:26 → 65
      LRR_4; Leucine Rich repeats (2 copies)
      pfam13855
      Location:25 → 84
      LRR_8; Leucine rich repeat
      cl13995
      Location:7 → 93
      MPP_superfamily; metallophosphatase superfamily, metallophosphatase domain

    RNA

    1. NR_131178.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate 5' exon structure, compared to variant 1. This variant is represented as non-coding because the predicted protein does not meet RefSeq quality criteria.
      Source sequence(s)
      AC012047, AC024603, AL136451, CR933639

    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
      75431624..76560168
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      76305674..77428762
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H2I8.1 GenPept UniProtKB/Swiss-Prot:Q9H2I8

    Gene LinkOut

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