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ZSWIM6 zinc finger SWIM-type containing 6 [ Homo sapiens (human) ]

Gene ID: 57688, updated on 5-Mar-2024

Summary

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Official Symbol
ZSWIM6provided by HGNC
Official Full Name
zinc finger SWIM-type containing 6provided by HGNC
Primary source
HGNC:HGNC:29316
See related
Ensembl:ENSG00000130449 MIM:615951; AllianceGenome:HGNC:29316
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
AFND; NEDMAGA
Summary
The protein encoded by this gene contains a zinc finger SWI2/SNF2 and MuDR (SWIM) domain. Proteins with SWIM domains have been found in a diverse number of species and are predicted to interact with DNA or proteins. Mutations in this gene result in acromelic frontonasal dysostosis. [provided by RefSeq, Apr 2017]
Expression
Ubiquitous expression in gall bladder (RPKM 6.8), brain (RPKM 6.4) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
5q12.1
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (61332258..61546172)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (62151402..62365278)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (60628085..60841999)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378993 Neighboring gene uncharacterized LOC105378994 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:60626175-60626745 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16045 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16046 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16047 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16048 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16049 Neighboring gene DEAD-box helicase 25 pseudogene Neighboring gene family with sequence similarity 133 member B pseudogene Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:60703838-60705037 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:60711419-60712045 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:60712046-60712673 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:60712674-60713300 Neighboring gene ribosomal protein L3 pseudogene 6 Neighboring gene long intergenic non-protein coding RNA 3122 Neighboring gene uncharacterized LOC101928651 Neighboring gene RNA, U6 small nuclear 913, pseudogene Neighboring gene heat shock protein family D (Hsp60) member 1 pseudogene 22

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. A Recurrent De Novo Nonsense Variant in ZSWIM6 Results in Severe Intellectual Disability without Frontonasal or Limb Malformations. Palmer EE, et al. Am J Hum Genet, 2017 Dec 7. PMID 29198722, Free PMC Article
  2. Acromelic frontonasal dysostosis and ZSWIM6 mutation: phenotypic spectrum and mosaicism. Twigg SR, et al. Clin Genet, 2016 Sep. PMID 26706854, Free PMC Article
  3. Classification of early age facial growth pattern and identification of the genetic basis in two Korean populations. Cha MY, et al. Sci Rep, 2022 Aug 15. PMID 35970861, Free PMC Article
  4. Altered gene expression in the subdivisions of the amygdala of Fyn-deficient mice as revealed by laser capture microdissection and mKIAA cDNA array analysis. Kai N, et al. Brain Res, 2006 Feb 16. PMID 16427614
  5. Exome sequencing identifies a recurrent de novo ZSWIM6 mutation associated with acromelic frontonasal dysostosis. Smith JD, et al. Am J Hum Genet, 2014 Aug 7. PMID 25105228, Free PMC Article

See all (21) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Classification of early age facial growth pattern and identification of the genetic basis in two Korean populations.
    Title: Classification of early age facial growth pattern and identification of the genetic basis in two Korean populations.
  2. This study builds support for a key role for ZSWIM6 in neuronal development and function, in addition to its putative roles in limb and craniofacial development, and provides a striking example of different variants in the same gene leading to distinct phenotypes.
    Title: A Recurrent De Novo Nonsense Variant in ZSWIM6 Results in Severe Intellectual Disability without Frontonasal or Limb Malformations.
  3. A single recurrent heterozygous missense substitution in ZSWIM6, encoding a protein of unknown function, was previously shown to underlie this disorder in four unrelated cases. Here we describe four additional individuals from three families, comprising two sporadic subjects (one of whom had no limb malformation) and a mildly affected female with a severely affected son
    Title: Acromelic frontonasal dysostosis and ZSWIM6 mutation: phenotypic spectrum and mosaicism.
  4. Exome sequencing of one trio and two unrelated probands revealed the same heterozygous variant (c.3487C>T [p. Arg1163Trp])associated with acromelic frontonasal dysostosis in a highly conserved protein domain of ZSWIM6; this variant has not been seen in the 1000 Genomes data, dbSNP, or the Exome Sequencing Project
    Title: Exome sequencing identifies a recurrent de novo ZSWIM6 mutation associated with acromelic frontonasal dysostosis.
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

Associated conditions

Description Tests
Acromelic frontonasal dysostosis
MedGen: C1863616 OMIM: 603671 GeneReviews: Not available
Compare labs
Neurodevelopmental disorder with movement abnormalities, abnormal gait, and autistic features
MedGen: C4693405 OMIM: 617865 GeneReviews: Not available
Compare labs

EBI GWAS Catalog

Description
Biological insights from 108 schizophrenia-associated genetic loci.
EBI GWAS Catalog
Genome-wide association analysis identifies 13 new risk loci for schizophrenia.
EBI GWAS Catalog
Genome-wide association study in a Swedish population yields support for greater CNV and MHC involvement in schizophrenia compared with bipolar disorder.
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

  • KIAA1577, DKFZp779P0344

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in striatal medium spiny neuron differentiation ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
part_of Cul2-RING ubiquitin ligase complex IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
zinc finger SWIM domain-containing protein 6
Names
zinc finger, SWIM domain containing 6

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_053150.1 RefSeqGene

    Range
    4986..218900
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_020928.2 → NP_065979.1  zinc finger SWIM domain-containing protein 6

    See identical proteins and their annotated locations for NP_065979.1

    Status: REVIEWED

    Source sequence(s)
    AA740254, AB046797, AC008836, AC122718, AW136453, BF750632, BF751445
    Consensus CDS
    CCDS47215.1
    UniProtKB/Swiss-Prot
    Q9HCJ5
    Related
    ENSP00000252744.5, ENST00000252744.6

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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    61332258..61546172
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047417453.1 → XP_047273409.1  zinc finger SWIM domain-containing protein 6 isoform X3

  2. XM_024446139.2 → XP_024301907.1  zinc finger SWIM domain-containing protein 6 isoform X1

  3. XM_017009677.2 → XP_016865166.1  zinc finger SWIM domain-containing protein 6 isoform X2

  4. XM_047417454.1 → XP_047273410.1  zinc finger SWIM domain-containing protein 6 isoform X4

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    62151402..62365278
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054353016.1 → XP_054208991.1  zinc finger SWIM domain-containing protein 6 isoform X1

  2. XM_054353018.1 → XP_054208993.1  zinc finger SWIM domain-containing protein 6 isoform X3

  3. XM_054353017.1 → XP_054208992.1  zinc finger SWIM domain-containing protein 6 isoform X2

  4. XM_054353019.1 → XP_054208994.1  zinc finger SWIM domain-containing protein 6 isoform X4

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9HCJ5.2 GenPept UniProtKB/Swiss-Prot:Q9HCJ5

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