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LOC110008580 Zic family member 2 polyalanine repeat instability region [ Homo sapiens (human) ]

Gene ID: 110008580, updated on 10-Oct-2023

Summary

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Gene symbol
LOC110008580
Gene description
Zic family member 2 polyalanine repeat instability region
Gene type
biological region
Feature type(s)
misc_feature: repeat_instability_region
repeat_region
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
This biological region is found within the coding region of the Zic family member 2 (ZIC2) gene on the q arm of chromosome 13. This region contains an imperfect trinucleotide repeat that encodes a polyalanine tract. Expansions and contractions of the imperfect repeat have been documented, and are associated with holoprosencephaly (HPE). A recurrent expansion that results in an expansion from 15 consecutive alanines to 25 consecutive alanines, may alter the DNA binding activity of the ZIC2 gene product. It has been suggested that expansions may be the result of somatic recombination between mispaired alleles, since the fathers of some affected individuals are mosaic carriers of the alanine expansion. [provided by RefSeq, Apr 2017]
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Genomic context

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Location:
13q32.3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (99985449..99985494)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (99196359..99196404)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (100637703..100637748)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene citramalyl-CoA lyase Neighboring gene CLYBL antisense RNA 3 Neighboring gene small nucleolar RNA U13 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:100461465-100461966 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:100461967-100462466 Neighboring gene ReSE screen-validated silencer GRCh37_chr13:100470112-100470282 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:100485830-100486582 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr13:100506615-100507814 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr13:100544348-100544902 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr13:100544903-100545456 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:100545457-100546010 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:100547191-100547692 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:100547693-100548192 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:100552816-100553392 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:100556702-100557202 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:100565623-100566124 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:100566125-100566624 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:100582975-100583475 Neighboring gene Sharpr-MPRA regulatory region 10052 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:100608499-100609474 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr13:100609475-100610449 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:100626468-100627010 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:100627011-100627551 Neighboring gene OCT4 hESC enhancer GRCh37_chr13:100631077-100631586 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5474 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5475 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr13:100635796-100636995 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:100642562-100643511 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:100649774-100650719 Neighboring gene Zic family member 5 Neighboring gene long intergenic non-protein coding RNA 554 Neighboring gene Zic family member 2 Neighboring gene NADH:ubiquinone oxidoreductase subunit A12 pseudogene 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. Phenotypic and molecular variability of the holoprosencephalic spectrum. Lazaro L, et al. Am J Med Genet A, 2004 Aug 15. PMID 15266610
  2. Polyalanine tract disorders and neurocognitive phenotypes. Shoubridge C, et al. Adv Exp Med Biol, 2012. PMID 23560312
  3. Single amino acid and trinucleotide repeats: function and evolution. Faux N. Adv Exp Med Biol, 2012. PMID 23560303
  4. Holoprosencephaly due to mutations in ZIC2: alanine tract expansion mutations may be caused by parental somatic recombination. Brown LY, et al. Hum Mol Genet, 2001 Apr 1. PMID 11285244
  5. Comparison of mutation findings in ZIC2 between microform and classical holoprosencephaly in a Brazilian cohort. Ribeiro LA, et al. Birth Defects Res A Clin Mol Teratol, 2012 Nov. PMID 22847929, Free PMC Article

See all (10) citations in PubMed

GeneRIFs: Gene References Into Functions

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See Variation Viewer (GRCh37.p13)

General gene information

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Other Names

  • ZIC2 polyalanine repeat instability region

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_053074.1 

    Range
    101..146
    Download
    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_000013.11 Reference GRCh38.p14 Primary Assembly

    Range
    99985449..99985494
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    99196359..99196404
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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