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LY6G6C lymphocyte antigen 6 family member G6C [ Homo sapiens (human) ]

Gene ID: 80740, updated on 3-Apr-2024

Summary

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Official Symbol
LY6G6Cprovided by HGNC
Official Full Name
lymphocyte antigen 6 family member G6Cprovided by HGNC
Primary source
HGNC:HGNC:13936
See related
Ensembl:ENSG00000204421 MIM:610435; AllianceGenome:HGNC:13936
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
G6c; NG24; C6orf24
Summary
LY6G6C belongs to a cluster of leukocyte antigen-6 (LY6) genes located in the major histocompatibility complex (MHC) class III region on chromosome 6. Members of the LY6 superfamily typically contain 70 to 80 amino acids, including 8 to 10 cysteines. Most LY6 proteins are attached to the cell surface by a glycosylphosphatidylinositol (GPI) anchor that is directly involved in signal transduction (Mallya et al., 2002 [PubMed 12079290]).[supplied by OMIM, Mar 2008]
Expression
Restricted expression toward skin (RPKM 160.9) See more
Orthologs
mouse all
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Genomic context

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Location:
6p21.33
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (31718648..31721746, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (31571681..31575898, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (31686425..31689523, complement)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene LY6G6F-LY6G6D readthrough Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:31681075-31681858 Neighboring gene lymphocyte antigen 6 family member G6E (pseudogene) Neighboring gene lymphocyte antigen 6 family member G6D Neighboring gene megakaryocyte and platelet inhibitory receptor G6b Neighboring gene DDAH family member 2, ADMA-independent Neighboring gene chloride intracellular channel 1 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:31701615-31702814 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:31704508-31705382

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. Genes encoding three new members of the leukocyte antigen 6 superfamily and a novel member of Ig superfamily, together with genes encoding the regulatory nuclear chloride ion channel protein (hRNCC) and an N omega-N omega-dimethylarginine dimethylaminohydrolase homologue, are found in a 30-kb segment of the MHC class III region. Ribas G, et al. J Immunol, 1999 Jul 1. PMID 10384126
  2. Transcriptional analysis of a novel cluster of LY-6 family members in the human and mouse major histocompatibility complex: five genes with many splice forms. Mallya M, et al. Genomics, 2002 Jul. PMID 12079290
  3. Characterization of the five novel Ly-6 superfamily members encoded in the MHC, and detection of cells expressing their potential ligands. Mallya M, et al. Protein Sci, 2006 Oct. PMID 17008713, Free PMC Article
  4. Analysis of the gene-dense major histocompatibility complex class III region and its comparison to mouse. Xie T, et al. Genome Res, 2003 Dec. PMID 14656967, Free PMC Article
  5. High-density SNP screening of the major histocompatibility complex in systemic lupus erythematosus demonstrates strong evidence for independent susceptibility regions. Barcellos LF, et al. PLoS Genet, 2009 Oct. PMID 19851445, Free PMC Article

See all (14) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
  2. Observational study of gene-disease association. (HuGE Navigator)
    Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
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

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

Function Evidence Code Pubs
enables identical protein binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Component Evidence Code Pubs
colocalizes_with external side of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
colocalizes_with external side of plasma membrane IDA
Inferred from Direct Assay
more info
 PubMed 
located_in extracellular region TAS
Traceable Author Statement
more info
  
located_in plasma membrane TAS
Traceable Author Statement
more info
  
part_of protein-containing complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of protein-containing complex IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
lymphocyte antigen 6 complex locus protein G6c
Names
lymphocyte antigen 6 complex, locus G6C
lymphocyte antigen-6 G6C

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_025261.3 → NP_079537.1  lymphocyte antigen 6 complex locus protein G6c precursor

    See identical proteins and their annotated locations for NP_079537.1

    Status: VALIDATED

    Source sequence(s)
    AL662899, AY359119, BC036302
    Consensus CDS
    CCDS4714.1
    UniProtKB/Swiss-Prot
    O95867, Q5SRS8, Q8IY94
    UniProtKB/TrEMBL
    A0A1U9X7Z1, A0A1U9X806
    Related
    ENSP00000364978.2, ENST00000375819.3

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
    31718648..31721746 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

  1. NT_113891.3 Reference GRCh38.p14 ALT_REF_LOCI_2

    Range
    3195936..3200153 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054329921.1 → XP_054185896.1  lymphocyte antigen 6 complex locus protein G6c isoform X1

    UniProtKB/Swiss-Prot
    O95867, Q5SRS8, Q8IY94
    UniProtKB/TrEMBL
    A0A1U9X7Z1

Reference GRCh38.p14 ALT_REF_LOCI_3

Genomic

  1. NT_167245.2 Reference GRCh38.p14 ALT_REF_LOCI_3

    Range
    2966410..2970627 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054330413.1 → XP_054186388.1  lymphocyte antigen 6 complex locus protein G6c isoform X1

    UniProtKB/Swiss-Prot
    O95867, Q5SRS8, Q8IY94
    UniProtKB/TrEMBL
    A0A1U9X7Z1

Reference GRCh38.p14 ALT_REF_LOCI_4

Genomic

  1. NT_167246.2 Reference GRCh38.p14 ALT_REF_LOCI_4

    Range
    3023694..3027911 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054330686.1 → XP_054186661.1  lymphocyte antigen 6 complex locus protein G6c isoform X1

    UniProtKB/Swiss-Prot
    O95867, Q5SRS8, Q8IY94
    UniProtKB/TrEMBL
    A0A1U9X7Z1

Reference GRCh38.p14 ALT_REF_LOCI_5

Genomic

  1. NT_167247.2 Reference GRCh38.p14 ALT_REF_LOCI_5

    Range
    3060523..3064740 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054330906.1 → XP_054186881.1  lymphocyte antigen 6 complex locus protein G6c isoform X1

    UniProtKB/Swiss-Prot
    O95867, Q5SRS8, Q8IY94
    UniProtKB/TrEMBL
    A0A1U9X7Z1

Reference GRCh38.p14 ALT_REF_LOCI_6

Genomic

  1. NT_167248.2 Reference GRCh38.p14 ALT_REF_LOCI_6

    Range
    2974462..2977560 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054331184.1 → XP_054187159.1  lymphocyte antigen 6 complex locus protein G6c isoform X2

Reference GRCh38.p14 ALT_REF_LOCI_7

Genomic

  1. NT_167249.2 Reference GRCh38.p14 ALT_REF_LOCI_7

    Range
    3017944..3022161 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054331426.1 → XP_054187401.1  lymphocyte antigen 6 complex locus protein G6c isoform X1

    UniProtKB/Swiss-Prot
    O95867, Q5SRS8, Q8IY94
    UniProtKB/TrEMBL
    A0A1U9X7Z1

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    31571681..31575898 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054356479.1 → XP_054212454.1  lymphocyte antigen 6 complex locus protein G6c isoform X1

    UniProtKB/Swiss-Prot
    O95867, Q5SRS8, Q8IY94
    UniProtKB/TrEMBL
    A0A1U9X7Z1
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O95867.1 GenPept UniProtKB/Swiss-Prot:O95867

Gene LinkOut

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