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UBAC2 UBA domain containing 2 [ Homo sapiens (human) ]

Gene ID: 337867, updated on 3-Apr-2024

Summary

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Official Symbol
UBAC2provided by HGNC
Official Full Name
UBA domain containing 2provided by HGNC
Primary source
HGNC:HGNC:20486
See related
Ensembl:ENSG00000134882 AllianceGenome:HGNC:20486
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
PHGDHL1
Summary
Involved in negative regulation of canonical Wnt signaling pathway and negative regulation of retrograde protein transport, ER to cytosol. Acts upstream of or within protein localization to endoplasmic reticulum. Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in testis (RPKM 8.2), thyroid (RPKM 7.2) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
13q32.3
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (99200854..99386504)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (98411009..98596811)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (99853108..100038758)

Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:99852081-99852734 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:99852735-99853386 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5469 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:99854040-99854691 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7931 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:99857838-99858338 Neighboring gene glyceraldehyde 3 phosphate dehydrogenase pseudogene 22 Neighboring gene UBAC2 antisense RNA 1 Neighboring gene RN7SK pseudogene 9 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7932 Neighboring gene H2A.Z histone pseudogene 3 Neighboring gene uncharacterized LOC124903198 Neighboring gene ReSE screen-validated silencer GRCh37_chr13:99914553-99914775 Neighboring gene G protein-coupled receptor 18 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5470 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:99955752-99956300 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:99956301-99956847 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr13:99966417-99967616 Neighboring gene G protein-coupled receptor 183 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:99994828-99995328 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:99995329-99995829 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7933 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7934 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7935 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7936 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7937 Neighboring gene FKSG29 Neighboring gene microRNA 623 Neighboring gene Sharpr-MPRA regulatory region 8816 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:100037611-100038229 Neighboring gene high mobility group box 3 pseudogene 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7938 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:100069445-100070364 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7939 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7940 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7941 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7942 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7943 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7944 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7945 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr13:100084644-100085843 Neighboring gene C-C motif chemokine receptor 12, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7947 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr13:100105623-100106122 Neighboring gene Sharpr-MPRA regulatory region 5830 Neighboring gene MPRA-validated peak2103 silencer Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr13:100147579-100148093 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7948 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7949 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7950 Neighboring gene long intergenic non-protein coding RNA 1232

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. Association between UBAC2 gene polymorphism and the risk of noise-induced hearing loss: a cross-sectional study. Wan L, et al. Environ Sci Pollut Res Int, 2022 May. PMID 35020141
  2. Replication study confirms the association between UBAC2 and Behçet's disease in two independent Chinese sets of patients and controls. Hou S, et al. Arthritis Res Ther, 2012 Mar 29. PMID 22455605, Free PMC Article
  3. A putative functional variant within the UBAC2 gene is associated with increased risk of Behçet's disease. Sawalha AH, et al. Arthritis Rheum, 2011 Nov. PMID 21918955, Free PMC Article
  4. UBAC2 promotes bladder cancer proliferation through BCRC-3/miRNA-182-5p/p27 axis. Gu C, et al. Cell Death Dis, 2020 Sep 10. PMID 32913183, Free PMC Article
  5. Genome-wide association study identifies novel alleles associated with risk of cutaneous basal cell carcinoma and squamous cell carcinoma. Nan H, et al. Hum Mol Genet, 2011 Sep 15. PMID 21700618, Free PMC Article

See all (70) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Association between UBAC2 gene polymorphism and the risk of noise-induced hearing loss: a cross-sectional study.
    Title: Association between UBAC2 gene polymorphism and the risk of noise-induced hearing loss: a cross-sectional study.
  2. UBAC2 promotes bladder cancer proliferation through BCRC-3/miRNA-182-5p/p27 axis.
    Title: UBAC2 promotes bladder cancer proliferation through BCRC-3/miRNA-182-5p/p27 axis.
  3. UBAC2 is associated with Behcet's disease in Chinese patients and implicates its involvement in transcriptional modulation.
    Title: Replication study confirms the association between UBAC2 and Behçet's disease in two independent Chinese sets of patients and controls.
  4. We established and confirmed the genetic association between UBAC2 and Behcet's disease in 3 independent sets of patients and controls
    Title: A putative functional variant within the UBAC2 gene is associated with increased risk of Behçet's disease.
  5. 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

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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
Genome-wide association study identifies novel alleles associated with risk of cutaneous basal cell carcinoma and squamous cell carcinoma.
EBI GWAS Catalog
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.
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

  • FLJ26351, FLJ30001, FLJ30548, FLJ42413, MGC90487

Gene Ontology Provided by GOA

Function Evidence Code Pubs
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 negative regulation of canonical Wnt signaling pathway IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in negative regulation of retrograde protein transport, ER to cytosol IMP
Inferred from Mutant Phenotype
more info
 PubMed 
acts_upstream_of_or_within protein localization to endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 PubMed 
Component Evidence Code Pubs
located_in endoplasmic reticulum IDA
Inferred from Direct Assay
more info
 PubMed 
located_in endoplasmic reticulum membrane IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
ubiquitin-associated domain-containing protein 2
Names
RP11-178C10.1
UBA domain-containing protein 2
phosphoglycerate dehydrogenase like 1
phosphoglycerate dehydrogenase-like protein 1

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_001144072.2 → NP_001137544.1  ubiquitin-associated domain-containing protein 2 isoform 1 precursor

    See identical proteins and their annotated locations for NP_001137544.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AI866141, AK075419, AK290342, AL136961, BC072674
    Consensus CDS
    CCDS45064.1
    UniProtKB/Swiss-Prot
    B3KNV7, Q0VAB5, Q5W0W6, Q5W0W9, Q6GQR2, Q6P4B0, Q8N2E8, Q8NBM4, Q96NW2
    UniProtKB/TrEMBL
    A8K2S7
    Related
    ENSP00000383911.3, ENST00000403766.8
    Conserved Domains (1) summary
    cd14305
    Location:305 → 342
    UBA_UBAC2; UBA domain found in ubiquitin-associated domain-containing protein 2 (UBAC2) and similar proteins

  2. NM_177967.4 → NP_808882.1  ubiquitin-associated domain-containing protein 2 isoform 2

    See identical proteins and their annotated locations for NP_808882.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) contains an alternate 5' end exon and is missing two consecutive in-frame coding exons compared to transcript variant 1. This results in a shorter isoform (2) with a different N-terminus compares to isoform 1.
    Source sequence(s)
    AI866141, AK054563, AL136961, AL159981, BC072674
    Consensus CDS
    CCDS9490.1
    UniProtKB/Swiss-Prot
    Q8NBM4
    Related
    ENSP00000365623.2, ENST00000376440.6
    Conserved Domains (1) summary
    cd14305
    Location:270 → 307
    UBA_UBAC2; UBA domain found in ubiquitin-associated domain-containing protein 2 (UBAC2) and similar proteins

RNA

  1. NR_026644.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) contains an alternate 5' end exon compared to transcript variant 1, which results in use of downstream translation start site and premature translation termination, rendering this transcript susceptible to nonsense-mediated mRNA decay (NMD). This transcript is sufficiently abundant to represent as a RefSeq record, however, the predicted protein is not represented because it is significantly truncated.
    Source sequence(s)
    AI866141, AK054563, AL136961, AL159981, BC072674, BC121139

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
    99200854..99386504
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011521083.3 → XP_011519385.1  ubiquitin-associated domain-containing protein 2 isoform X2

    Conserved Domains (1) summary
    cd14305
    Location:253 → 290
    UBA_UBAC2; UBA domain found in ubiquitin-associated domain-containing protein 2 (UBAC2) and similar proteins

  2. XM_011521082.3 → XP_011519384.2  ubiquitin-associated domain-containing protein 2 isoform X1

  3. XM_047430286.1 → XP_047286242.1  ubiquitin-associated domain-containing protein 2 isoform X3

    Related
    ENST00000494576.5

  4. XM_017020553.2 → XP_016876042.1  ubiquitin-associated domain-containing protein 2 isoform X4

    Conserved Domains (1) summary
    cd14305
    Location:135 → 172
    UBA_UBAC2; UBA domain found in ubiquitin-associated domain-containing protein 2 (UBAC2) and similar proteins

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060937.1 Alternate T2T-CHM13v2.0

    Range
    98411009..98596811
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054374488.1 → XP_054230463.1  ubiquitin-associated domain-containing protein 2 isoform X2

  2. XM_054374487.1 → XP_054230462.1  ubiquitin-associated domain-containing protein 2 isoform X1

  3. XM_054374489.1 → XP_054230464.1  ubiquitin-associated domain-containing protein 2 isoform X3

  4. XM_054374490.1 → XP_054230465.1  ubiquitin-associated domain-containing protein 2 isoform X4

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8NBM4.1 GenPept UniProtKB/Swiss-Prot:Q8NBM4

Gene LinkOut

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

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