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KIR3DP1 killer cell immunoglobulin like receptor, three Ig domains pseudogene 1 [ Homo sapiens (human) ]

Gene ID: 548594, updated on 8-Nov-2023

Summary

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Official Symbol
KIR3DP1provided by HGNC
Official Full Name
killer cell immunoglobulin like receptor, three Ig domains pseudogene 1provided by HGNC
Primary source
HGNC:HGNC:16343
See related
Ensembl:ENSG00000264257 MIM:610604; AllianceGenome:HGNC:16343
Gene type
pseudo
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
KIRX; KIR48; CD158c; KIR2DS6; KIR3DS2P
Summary
Killer cell immunoglobulin-like receptors (KIRs) are transmembrane glycoproteins expressed by natural killer cells and subsets of T cells. The KIR genes are polymorphic and highly homologous and they are found in a cluster on chromosome 19q13.4 within the 1 Mb leukocyte receptor complex (LRC). The gene content of the KIR gene cluster varies among haplotypes, although several "framework" genes are found in all haplotypes (KIR3DL3, KIR3DP1, KIR3DL4, KIR3DL2). The KIR proteins are classified by the number of extracellular immunoglobulin domains (2D or 3D) and by whether they have a long (L) or short (S) cytoplasmic domain. KIR proteins with the long cytoplasmic domain transduce inhibitory signals upon ligand binding via an immune tyrosine-based inhibitory motif (ITIM), while KIR proteins with the short cytoplasmic domain lack the ITIM motif and instead associate with the TYRO protein tyrosine kinase binding protein to transduce activating signals. The ligands for several KIR proteins are subsets of HLA class I molecules; thus, KIR proteins are thought to play an important role in regulation of the immune response. This gene is one of the "framework" loci that is present on all haplotypes. This gene is considered to be a pseudogene based on the absence of transcription and it lacks several functional domains compared to other killer cell immunoglobulin-like receptors. A rare haplotype, the result of a recombinantion event, has two copies of this gene, one of which may encode a secreted protein. (PMID: 15580659)[provided by RefSeq, Mar 2011]
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Genomic context

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See KIR3DP1 in Genome Data Viewer
Location:
19q13.42
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (54786362..54790418)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (57880635..57884691)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (55297814..55301870)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene killer cell immunoglobulin like receptor, two Ig domains pseudogene 1 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr19:55275257-55276456 Neighboring gene uncharacterized LOC101928804 Neighboring gene killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 1 Neighboring gene killer cell immunoglobulin like receptor, two Ig domains and long cytoplasmic tail 4 Neighboring gene killer cell immunoglobulin like receptor, three Ig domains and long cytoplasmic tail 1

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Bibliography

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Related articles in PubMed

  1. Analysis of KIR3DP1 Polymorphism Provides Relevant Information on Centromeric KIR Gene Content. Bono M, et al. J Immunol, 2018 Sep 1. PMID 30068594
  2. Killer cell immunoglobulin-like receptor genotypes in Behçet's disease patients: any role for the 3DP1*001/002 pseudogene? Arayssi TK, et al. Genet Test Mol Biomarkers, 2009 Jun. PMID 19405872
  3. Comparative genomic analysis, diversity and evolution of two KIR haplotypes A and B. Martin AM, et al. Gene, 2004 Jun 23. PMID 15194195
  4. Partial duplication of chromosome 19 associated with syndromic duane retraction syndrome. Abu-Amero KK, et al. Ophthalmic Genet, 2015 Mar. PMID 23952617
  5. The silent KIR3DP1 gene (CD158c) is transcribed and might encode a secreted receptor in a minority of humans, in whom the KIR3DP1, KIR2DL4 and KIR3DL1/KIR3DS1 genes are duplicated. Gómez-Lozano N, et al. Eur J Immunol, 2005 Jan. PMID 15580659

See all (43) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. KIR3DP1 polymorphism analysis also provides information to dissect between Cen-B1/Cen-B1 and Cen-B1/Cen-B2 donors. Taken together, our data suggest that the analysis of KIR3DP1 polymorphism should be included in KIR repertoire evaluation.
    Title: Analysis of KIR3DP1 Polymorphism Provides Relevant Information on Centromeric KIR Gene Content.
  2. Array CGH showed a 95 Kb de novo duplication on chromosome 19q13.4 encompassing four killer cell immunoglobulin-like receptor (KIR) genes.
    Title: Partial duplication of chromosome 19 associated with syndromic duane retraction syndrome.
  3. Observational study of gene-disease association and gene-gene interaction. (HuGE Navigator)
    Title: Killer cell immunoglobulin-like receptor gene-cluster 3DS1-2DL5-2DS1-2DS5 predisposes susceptibility to Vogt-Koyanagi-Harada syndrome in Japanese individuals.
  4. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
    Title: Effect of killer immunoglobulin-like receptors in the response to combined treatment in patients with chronic hepatitis C virus infection.
  5. Authors speculate on any role for KIR3DP1 pseudogene in Lebanese Behcet disease patients.
    Title: Killer cell immunoglobulin-like receptor genotypes in Behçet's disease patients: any role for the 3DP1*001/002 pseudogene?
  6. Observational study of gene-disease association. (HuGE Navigator)
    Title: Association of KIR2DS1 and KIR2DS3 with fatal outcome in Ebola virus infection.
  7. Observational study of genotype prevalence. (HuGE Navigator)
    Title: Diversity of killer cell immunoglobulin-like receptor genes in Indonesian populations of Sumatra, Sulawesi and Moluccas Islands.
  8. 4.5% of the individuals of a Caucasoid population bear a recombinant allele of KIR3DP1, officially designed KIR3DP1*004, that associates tightly with gene duplications of KIR3DP1, KIR2DL4 and KIR3DL1/KIR3DS1.
    Title: The silent KIR3DP1 gene (CD158c) is transcribed and might encode a secreted receptor in a minority of humans, in whom the KIR3DP1, KIR2DL4 and KIR3DL1/KIR3DS1 genes are duplicated.
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Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Other Names

  • killer cell immunoglobulin-like receptor, three domains, pseudogene 1
  • killer-cell Ig-like receptor pseudogene

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_005994.1 

    Range
    106823..110875
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    GenBank, FASTA, Sequence Viewer (Graphics)

  2. NG_033792.1 

    Range
    101..4157
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    GenBank, FASTA, Sequence Viewer (Graphics)

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
    54786362..54790418
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_016107300.1 Reference GRCh38.p14 PATCHES

    Range
    87995..92051
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_016107301.1 Reference GRCh38.p14 PATCHES

    Range
    88002..92058
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_016107302.1 Reference GRCh38.p14 PATCHES

    Range
    87969..92025
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_016107303.1 Reference GRCh38.p14 PATCHES

    Range
    87959..92017
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_016107304.1 Reference GRCh38.p14 PATCHES

    Range
    87972..92028
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Reference GRCh38.p14 PATCHES

Genomic

  1. NW_016107305.1 Reference GRCh38.p14 PATCHES

    Range
    87957..92013
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_016107306.1 Reference GRCh38.p14 PATCHES

    Range
    87782..91834
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_016107307.1 Reference GRCh38.p14 PATCHES

    Range
    87930..91986
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Reference GRCh38.p14 PATCHES

Genomic

  1. NW_016107309.1 Reference GRCh38.p14 PATCHES

    Range
    87969..92025
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Reference GRCh38.p14 PATCHES

Genomic

  1. NW_016107310.1 Reference GRCh38.p14 PATCHES

    Range
    118351..122403
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Reference GRCh38.p14 ALT_REF_LOCI_1

Genomic

  1. NW_003571054.1 Reference GRCh38.p14 ALT_REF_LOCI_1

    Range
    692021..696077
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Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

  1. NW_003571055.2 Reference GRCh38.p14 ALT_REF_LOCI_2

    Range
    404220..408276
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Reference GRCh38.p14 ALT_REF_LOCI_7

Genomic

  1. NW_003571060.1 Reference GRCh38.p14 ALT_REF_LOCI_7

    Range
    690696..694752
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Reference GRCh38.p14 ALT_REF_LOCI_8

Genomic

  1. NW_003571061.2 Reference GRCh38.p14 ALT_REF_LOCI_8

    Range
    497310..503730
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Reference GRCh38.p14 ALT_REF_LOCI_9

Genomic

  1. NT_187693.1 Reference GRCh38.p14 ALT_REF_LOCI_9

    Range
    768928..772984
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Reference GRCh38.p14 ALT_REF_LOCI_10

Genomic

  1. NT_187636.1 Reference GRCh38.p14 ALT_REF_LOCI_10

    Range
    112330..116382 complement
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_11

Genomic

  1. NT_187637.1 Reference GRCh38.p14 ALT_REF_LOCI_11

    Range
    78421..82477 complement
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_13

Genomic

  1. NT_187639.1 Reference GRCh38.p14 ALT_REF_LOCI_13

    Range
    78990..83046 complement
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_14

Genomic

  1. NT_187640.1 Reference GRCh38.p14 ALT_REF_LOCI_14

    Range
    67790..71842 complement
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_15

Genomic

  1. NT_187641.1 Reference GRCh38.p14 ALT_REF_LOCI_15

    Range
    118007..122063 complement
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_17

Genomic

  1. NT_187643.1 Reference GRCh38.p14 ALT_REF_LOCI_17

    Range
    78681..82737 complement
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_19

Genomic

  1. NT_187645.1 Reference GRCh38.p14 ALT_REF_LOCI_19

    Range
    78697..82753 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_20

Genomic

  1. NT_187668.1 Reference GRCh38.p14 ALT_REF_LOCI_20

    Range
    68583..72639 complement
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_21

Genomic

  1. NT_187669.1 Reference GRCh38.p14 ALT_REF_LOCI_21

    Range
    78681..82737 complement
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    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_23

Genomic

  1. NT_187671.1 Reference GRCh38.p14 ALT_REF_LOCI_23

    Range
    65274..69330
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Reference GRCh38.p14 ALT_REF_LOCI_24

Genomic

  1. NT_187672.1 Reference GRCh38.p14 ALT_REF_LOCI_24

    Range
    87940..91996
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Reference GRCh38.p14 ALT_REF_LOCI_25

Genomic

  1. NT_187673.1 Reference GRCh38.p14 ALT_REF_LOCI_25

    Range
    78660..82716 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_26

Genomic

  1. NT_187674.1 Reference GRCh38.p14 ALT_REF_LOCI_26

    Range
    73200..77256
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Reference GRCh38.p14 ALT_REF_LOCI_27

Genomic

  1. NT_187675.1 Reference GRCh38.p14 ALT_REF_LOCI_27

    Range
    129368..133420
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Reference GRCh38.p14 ALT_REF_LOCI_28

Genomic

  1. NT_187676.1 Reference GRCh38.p14 ALT_REF_LOCI_28

    Range
    62276..66332
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Reference GRCh38.p14 ALT_REF_LOCI_30

Genomic

  1. NT_187683.1 Reference GRCh38.p14 ALT_REF_LOCI_30

    Range
    60538..64594
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Reference GRCh38.p14 ALT_REF_LOCI_32

Genomic

  1. NT_187685.1 Reference GRCh38.p14 ALT_REF_LOCI_32

    Range
    78173..82229 complement
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Reference GRCh38.p14 ALT_REF_LOCI_33

Genomic

  1. NT_187686.1 Reference GRCh38.p14 ALT_REF_LOCI_33

    Range
    79022..83078 complement
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Reference GRCh38.p14 ALT_REF_LOCI_34

Genomic

  1. NT_187687.1 Reference GRCh38.p14 ALT_REF_LOCI_34

    Range
    78485..82541 complement
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    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    57880635..57884691
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Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NG_005783.1: Suppressed sequence

    Description
    NG_005783.1: This RefSeq was permanently suppressed since this pseudogene is currently represented on the KIR gene cluster, haplotype A on chromosome 19.

  2. NM_001015070.1: Suppressed sequence

    Description
    NM_001015070.1: This RefSeq was permanently suppressed because it is now thought that this gene is a pseudogene.
Nucleotide Protein
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