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LYPD5 LY6/PLAUR domain containing 5 [ Homo sapiens (human) ]

Gene ID: 284348, updated on 5-Mar-2024

Summary

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Official Symbol
LYPD5provided by HGNC
Official Full Name
LY6/PLAUR domain containing 5provided by HGNC
Primary source
HGNC:HGNC:26397
See related
Ensembl:ENSG00000159871 MIM:619618; AllianceGenome:HGNC:26397
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
PRO4356; HALDISIN
Summary
Predicted to be located in extracellular region. Predicted to be active in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in skin (RPKM 12.1), brain (RPKM 2.5) and 5 other tissues See more
Orthologs
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Genomic context

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Location:
19q13.31
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (43795927..43820634, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (46618728..46643530, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (44300079..44324786, complement)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene SMG9 nonsense mediated mRNA decay factor Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10728 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14736 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10729 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:44268619-44268844 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14737 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14738 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14739 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:44270408-44270571 Neighboring gene CRISPRi-validated cis-regulatory element KCNN4 K1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:44281957-44282457 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10730 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:44283513-44284012 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14740 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10731 Neighboring gene potassium calcium-activated channel subfamily N member 4 Neighboring gene CRISPRi-validated cis-regulatory element chr19.4589 Neighboring gene Sharpr-MPRA regulatory region 14970 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:44288851-44289352 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:44289353-44289852 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14743 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14744 Neighboring gene zinc finger protein 283 Neighboring gene zinc finger protein 404

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. The urokinase receptor homolog Haldisin is a novel differentiation marker of stratum granulosum in squamous epithelia. Gårdsvoll H, et al. J Histochem Cytochem, 2013 Nov. PMID 23896969, Free PMC Article
  2. Expression of the Ly6/uPAR-domain proteins C4.4A and Haldisin in non-invasive and invasive skin lesions. Kriegbaum MC, et al. J Histochem Cytochem, 2015 Feb. PMID 25414274, Free PMC Article
  3. The correlation between reading and mathematics ability at age twelve has a substantial genetic component. Davis OS, et al. Nat Commun, 2014 Jul 8. PMID 25003214, Free PMC Article
  4. Large-scale genotyping identifies 41 new loci associated with breast cancer risk. Michailidou K, et al. Nat Genet, 2013 Apr. PMID 23535729, Free PMC Article
  5. A proteome-scale map of the SARS-CoV-2-human contactome. Kim DK, et al. Nat Biotechnol, 2023 Jan. PMID 36217029, Free PMC Article

See all (18) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Expression of the Ly6/uPAR-domain proteins C4.4A and Haldisin in non-invasive and invasive skin lesions
    Title: Expression of the Ly6/uPAR-domain proteins C4.4A and Haldisin in non-invasive and invasive skin lesions.
  2. The study identifies LYPD5 a novel differentiation marker of stratum granulosum in squamous epithelia.
    Title: The urokinase receptor homolog Haldisin is a novel differentiation marker of stratum granulosum in squamous epithelia.
  3. 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.
  4. 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

EBI GWAS Catalog

Description
Large-scale genotyping identifies 41 new loci associated with breast cancer risk.
EBI GWAS Catalog
The correlation between reading and mathematics ability at age twelve has a substantial genetic component.
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

  • FLJ30469

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Component Evidence Code Pubs
located_in extracellular region TAS
Traceable Author Statement
more info
  
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane TAS
Traceable Author Statement
more info
  
located_in side of membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
ly6/PLAUR domain-containing protein 5
Names
human antigen with LU-domains expressed in skin
metastasis-associated protein

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_001031749.3 → NP_001026919.2  ly6/PLAUR domain-containing protein 5 isoform A precursor

    See identical proteins and their annotated locations for NP_001026919.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (A) encodes the longer protein (isoform A).
    Source sequence(s)
    AC115522, AY358719, BC044237, BC057816, CF529795, DC364960
    Consensus CDS
    CCDS46096.1
    UniProtKB/Swiss-Prot
    Q6PEX9, Q6UWN5, Q96DR2
    UniProtKB/TrEMBL
    B4DWV3
    Related
    ENSP00000367185.2, ENST00000377950.8
    Conserved Domains (1) summary
    pfam00021
    Location:135 → 214
    UPAR_LY6; u-PAR/Ly-6 domain

  2. NM_001288763.2 → NP_001275692.1  ly6/PLAUR domain-containing protein 5 isoform B

    See identical proteins and their annotated locations for NP_001275692.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (C) contains a distinct 5' UTR, lacks an in-frame portion of the 5' coding region and initiates translation at a downstream start codon compared to variant 1. The encoded protein (isoform B) has a distinct N-terminus and is shorter than isoform A. Variants B and C encode the same protein.
    Source sequence(s)
    AC115522, BC044237, CF529795, CK823626, DA093306
    Consensus CDS
    CCDS12631.1
    UniProtKB/TrEMBL
    B4DWV3
    Related
    ENSP00000471692.1, ENST00000594013.5
    Conserved Domains (1) summary
    pfam00021
    Location:92 → 171
    UPAR_LY6; u-PAR/Ly-6 domain

  3. NM_182573.3 → NP_872379.2  ly6/PLAUR domain-containing protein 5 isoform B

    See identical proteins and their annotated locations for NP_872379.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (B) contains an alternate exon in the 5' UTR, lacks a portion of the 5' coding region, and initiates translation at a downstream start codon compared to variant 1. The encoded protein (isoform B) has a distinct N-terminus and is shorter than isoform A. Variants B and C encode the same protein.
    Source sequence(s)
    AC115522, BC044237, CF529795, DA286806
    Consensus CDS
    CCDS12631.1
    UniProtKB/TrEMBL
    B4DWV3
    Related
    ENSP00000408433.1, ENST00000414615.6
    Conserved Domains (1) summary
    pfam00021
    Location:92 → 171
    UPAR_LY6; u-PAR/Ly-6 domain

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_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    43795927..43820634 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    46618728..46643530 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6UWN5.2 GenPept UniProtKB/Swiss-Prot:Q6UWN5

Gene LinkOut

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