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

Gene ID: 83938, updated on 2-Nov-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
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Genomic context

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See LRMDA in Genome Data Viewer
Location:
10q22.2-q22.3
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (75431624..76560168)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (76305674..77428762)
RS_2024_09 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 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. 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
  2. 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
  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 (19) 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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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Oculocutaneous albinism type 7
MedGen: C3808786 OMIM: 615179 GeneReviews: Oculocutaneous Albinism and Ocular Albinism Overview
not available

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 Variation Viewer (GRCh37.p13)

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_2024_08

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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