U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

SHISA6 shisa family member 6 [ Homo sapiens (human) ]

Gene ID: 388336, updated on 7-Apr-2024

Summary

Go to the top of the page Help
Official Symbol
SHISA6provided by HGNC
Official Full Name
shisa family member 6provided by HGNC
Primary source
HGNC:HGNC:34491
See related
Ensembl:ENSG00000188803 MIM:617327; AllianceGenome:HGNC:34491
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
Summary
Predicted to enable ionotropic glutamate receptor binding activity. Predicted to be involved in several processes, including excitatory chemical synaptic transmission; regulation of short-term neuronal synaptic plasticity; and regulation of signal transduction. Predicted to be located in asymmetric, glutamatergic, excitatory synapse. Predicted to be part of AMPA glutamate receptor complex. Predicted to be active in glutamatergic synapse; postsynaptic density; and synaptic membrane. Predicted to be integral component of postsynaptic density membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Biased expression in brain (RPKM 3.7), endometrium (RPKM 2.0) and 9 other tissues See more
Orthologs
mouse all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
Location:
17p12
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (11241213..11564063)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (11149418..11472179)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (11144530..11467380)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105371536 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:10829767-10830266 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:11053466-11054665 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:11102854-11104053 Neighboring gene RNA, 7SL, cytoplasmic 601, pseudogene Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:11148155-11148656 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:11161596-11161784 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:11177103-11177604 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:11200213-11200381 Neighboring gene uncharacterized LOC124903929 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr17:11397143-11397680 Neighboring gene NANOG hESC enhancer GRCh37_chr17:11406563-11407064 Neighboring gene MPRA-validated peak2723 silencer Neighboring gene MPRA-validated peak2724 silencer Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:11540697-11541896 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:11571267-11572208 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:11572478-11573677 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:11602804-11604003 Neighboring gene dynein axonemal heavy chain 9 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr17:11639660-11640859 Neighboring gene uncharacterized LOC101928350 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:11812057-11812249 Neighboring gene NANOG hESC enhancer GRCh37_chr17:11831780-11832352 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:11851561-11852062 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:11852063-11852562 Neighboring gene uncharacterized LOC124903928

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • 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

Go to the top of the pageHelp

Related articles in PubMed

  1. Genetic variants in the SHISA6 gene are associated with delayed cognitive impairment in two family datasets. Ramos J, et al. Alzheimers Dement, 2023 Feb. PMID 35490390, Free PMC Article
  2. Genome-wide meta-analyses of multiancestry cohorts identify multiple new susceptibility loci for refractive error and myopia. Verhoeven VJ, et al. Nat Genet, 2013 Mar. PMID 23396134, Free PMC Article
  3. Shared genetic susceptibility to ischemic stroke and coronary artery disease: a genome-wide analysis of common variants. Dichgans M, et al. Stroke, 2014 Jan. PMID 24262325, Free PMC Article
  4. Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers. Lauc G, et al. PLoS Genet, 2013. PMID 23382691, Free PMC Article
  5. Competitive binding of E3 ligases TRIM26 and WWP2 controls SOX2 in glioblastoma. Mahlokozera T, et al. Nat Commun, 2021 Nov 3. PMID 34732716, Free PMC Article

See all (13) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Genetic variants in the SHISA6 gene are associated with delayed cognitive impairment in two family datasets.
    Title: Genetic variants in the SHISA6 gene are associated with delayed cognitive impairment in two family datasets.
  2. 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.
Submit: New GeneRIF Correction

Phenotypes

Go to the top of the page Help

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
Genome-wide meta-analyses of multiancestry cohorts identify multiple new susceptibility loci for refractive error and myopia.
EBI GWAS Catalog
Loci associated with N-glycosylation of human immunoglobulin G show pleiotropy with autoimmune diseases and haematological cancers.
EBI GWAS Catalog
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
EBI GWAS Catalog
Shared genetic susceptibility to ischemic stroke and coronary artery disease: a genome-wide analysis of common variants.
EBI GWAS Catalog

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

Markers

Homology

Clone Names

  • FLJ37030, FLJ37733, FLJ45455

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables PDZ domain binding IEA
Inferred from Electronic Annotation
more info
  
enables ionotropic glutamate receptor binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in Wnt signaling pathway IEA
Inferred from Electronic Annotation
more info
  
involved_in excitatory chemical synaptic transmission ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in negative regulation of canonical Wnt signaling pathway ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in postsynaptic neurotransmitter receptor diffusion trapping IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of AMPA glutamate receptor clustering ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in regulation of AMPA receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in regulation of short-term neuronal synaptic plasticity IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in spermatogenesis ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
part_of AMPA glutamate receptor complex IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in asymmetric, glutamatergic, excitatory synapse ISS
Inferred from Sequence or Structural Similarity
more info
  
is_active_in dendritic spine membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
is_active_in postsynaptic density IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in postsynaptic density ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in postsynaptic density membrane IEA
Inferred from Electronic Annotation
more info
  
is_active_in postsynaptic membrane IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

Go to the top of the page Help
Preferred Names
protein shisa-6
Names
protein shisa-6 homolog
shisa homolog 6

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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_001173461.2 → NP_001166932.1  protein shisa-6 isoform 2 precursor

    See identical proteins and their annotated locations for NP_001166932.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate exon in the coding region, compared to variant 1. The resulting isoform (2) lacks an internal segment, compared to isoform 1.
    Source sequence(s)
    AC005725, AC007510
    Consensus CDS
    CCDS54090.1
    UniProtKB/Swiss-Prot
    B3KXV5, Q4PL63, Q6ZSJ9
    Related
    ENSP00000387157.3, ENST00000409168.7
    Conserved Domains (1) summary
    pfam13908
    Location:92 → 273
    Shisa; Wnt and FGF inhibitory regulator

  2. NM_001173462.2 → NP_001166933.1  protein shisa-6 isoform 3 precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an alternate exon in the coding region, compared to variant 1. The resulting isoform (3) lacks an internal segment, compared to isoform 1.
    Source sequence(s)
    AC005725, AC007510
    Consensus CDS
    CCDS54089.1
    UniProtKB/Swiss-Prot
    Q6ZSJ9
    Related
    ENSP00000388659.3, ENST00000432116.7

  3. NM_207386.4 → NP_997269.2  protein shisa-6 isoform 1 precursor

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC005725, AC007510, AK128003, DA362563
    Consensus CDS
    CCDS45615.1
    UniProtKB/Swiss-Prot
    Q6ZSJ9
    Related
    ENSP00000390084.3, ENST00000441885.8
    Conserved Domains (1) summary
    pfam13908
    Location:91 → 258
    Shisa; Wnt and FGF inhibitory regulator

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_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    11241213..11564063
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    11149418..11472179
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_175903.2: Suppressed sequence

    Description
    NM_175903.2: This RefSeq was permanently suppressed because it is primarily UTR sequence.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q6ZSJ9.2 GenPept UniProtKB/Swiss-Prot:Q6ZSJ9

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous